Running as unit: rb-build-amd64_2-54672.service; invocation ID: 58c11f35aa914f28b95104efd2baa31d ==================================================================================== Thu Sep 18 14:47:49 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_2) on jenkins, called using "ionos5-amd64 ionos1-amd64" as arguments. Thu Sep 18 14:47:49 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-UisWDV3F" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 14:47:50 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Sep 18 14:47:50 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-1uTlyU' Thu Sep 18 14:47:50 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Sep 18 14:47:50 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-BYeuaf' ok, let's check if gmap is building anywhere yet… ok, gmap is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of gmap in forky on amd64 on jenkins now. 1st build will be done on ionos5-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Thu Sep 18 14:47:57 UTC 2025 I: starting to build gmap/forky/amd64 on jenkins on '2025-09-18 14:47' Thu Sep 18 14:47:57 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_2/54672/console.log 1758206877 amd64 forky gmap Thu Sep 18 14:47:57 UTC 2025 I: Downloading source for forky/gmap=2024-11-20+ds-2 --2025-09-18 14:47:57-- http://deb.debian.org/debian/pool/main/g/gmap/gmap_2024-11-20%2bds-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2309 (2.3K) [text/prs.lines.tag] Saving to: ‘gmap_2024-11-20+ds-2.dsc’ 0K .. 100% 239M=0s 2025-09-18 14:47:57 (239 MB/s) - ‘gmap_2024-11-20+ds-2.dsc’ saved [2309/2309] --2025-09-18 14:47:57-- http://deb.debian.org/debian/pool/main/g/gmap/gmap_2024-11-20%2bds-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2309 (2.3K) [text/prs.lines.tag] Saving to: ‘gmap_2024-11-20+ds-2.dsc’ 0K .. 100% 239M=0s 2025-09-18 14:47:57 (239 MB/s) - ‘gmap_2024-11-20+ds-2.dsc’ saved [2309/2309] Thu Sep 18 14:47:57 UTC 2025 I: gmap_2024-11-20+ds-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gmap Binary: gmap Architecture: any Version: 2024-11-20+ds-2 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille , Alexandre Mestiashvili , Étienne Mollier Homepage: http://research-pub.gene.com/gmap Standards-Version: 4.7.1 Vcs-Browser: https://salsa.debian.org/med-team/gmap Vcs-Git: https://salsa.debian.org/med-team/gmap.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, help2man, libbz2-dev, zlib1g-dev, debhelper, libsimde-dev Package-List: gmap deb science optional arch=any Checksums-Sha1: 62abf6c57d47832f38718b9aaf5187e159257084 2578616 gmap_2024-11-20+ds.orig.tar.xz a946ded506b5dba688b371e3b16faf7539ebcb89 14076 gmap_2024-11-20+ds-2.debian.tar.xz Checksums-Sha256: 82d456442f2249c7c0e3a6bf9cfe3a2cc9b9e434bd9705ac6c0a38f7b01011cd 2578616 gmap_2024-11-20+ds.orig.tar.xz a46f8e7a62e51afe01d27aeb6f56645eb5d90c86864f00a7334eaf308560fee4 14076 gmap_2024-11-20+ds-2.debian.tar.xz Files: e39b9b6d94d52610760153750fcdb512 2578616 gmap_2024-11-20+ds.orig.tar.xz a64a838fc92226d815d91a6cb3a9b86c 14076 gmap_2024-11-20+ds-2.debian.tar.xz Dgit: 6d6d76dbf92b45dc9bd68bd130388cb2de40ec81 debian archive/debian/2024-11-20+ds-2 https://git.dgit.debian.org/gmap -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAme+Ql0UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdr9bBAAu85nh1jaMUb7FdVvkfUwYWetv/Z/ yn+4097h9PY42IH6w0H0VncSdI1rKa9pMJmq1PnNo15JGaEt5Sg8Mv5kWRFDZr8H UTGhGR1gR0MAlqo/2+VDioCCCR3dpH8vX6A69GVxqGGtgcKYleVVoh/Sy1Pf7amF r1gMf/VPTPR7yrUHKlV4B5aBV3gMCPAp0yo10P9/4IX5Jye9AwiI4gkJTZAqs5mX 9OYse7Lz/OTS6EmK5+F34fhiCY/5O04ro1UmlMlCmJlxEnppTAoRA6Px9NjLmomK wAwq47RmWz40yGTEluH8GH9FGGdkXRgybEgqPUtwQaY6vabQYn+doENjqufn6TzY MQ7UBQtGEQCdMfjq7pFVYyoarAMwGmRXlQO8whsdK2I4B10QNTRuj4WdLLKqmg0I vzRaEWy9NoLMQTgWCLaXZD1RJIM06DFHBaJj25D6uelmZmjTmdQ92OAstVEvLHOd MThtwvYe3isXgxF3V4oFbxKD9Wl7sQxKznSDkmAHkqzbFawN73Xg/FM1TlAGqD+F C6WvqcqhfEOtMsGtDOxuq+XTya51E4zw5dGQe76FP2g+veOzl3VXFxSK+FggPGE7 xBi3rJFTY2HGSkfp6tPCptA6HR0ErncRUrAgEewXp4SwB9llYHQb1fIYri7tXqZC xaH5pwF5yDkMlYw= =kiYB -----END PGP SIGNATURE----- Thu Sep 18 14:47:57 UTC 2025 I: Checking whether the package is not for us Thu Sep 18 14:47:57 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Thu Sep 18 14:47:57 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Thu Sep 18 14:47:57 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Sep 18 14:47:57 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-iKOxvW' ==================================================================================== Wed Oct 21 21:10:58 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 gmap forky /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI 2024-11-20+ds-2" as arguments. Wed Oct 21 21:10:58 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-045TjmKe" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Oct 21 21:10:58 UTC 2026 I: Downloading source for forky/gmap=2024-11-20+ds-2 Reading package lists... NOTICE: 'gmap' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gmap.git Please use: git clone https://salsa.debian.org/med-team/gmap.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2595 kB of source archives. Get:1 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (dsc) [2309 B] Get:2 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (tar) [2579 kB] Get:3 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (diff) [14.1 kB] Fetched 2595 kB in 0s (45.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'gmap' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gmap.git Please use: git clone https://salsa.debian.org/med-team/gmap.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2595 kB of source archives. Get:1 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (dsc) [2309 B] Get:2 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (tar) [2579 kB] Get:3 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (diff) [14.1 kB] Fetched 2595 kB in 0s (45.4 MB/s) Download complete and in download only mode ============================================================================= Building gmap in forky on amd64 on ionos5-amd64 now. Date: Wed Oct 21 21:10:58 UTC 2026 Date UTC: Wed Oct 21 21:10:58 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 21 09:10:58 -12 2026 I: pbuilder-time-stamp: 1792617058 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gmap_2024-11-20+ds-2.dsc] I: copying [./gmap_2024-11-20+ds.orig.tar.xz] I: copying [./gmap_2024-11-20+ds-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gmap_2024-11-20+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting gmap in gmap-2024-11-20+ds dpkg-source: info: unpacking gmap_2024-11-20+ds.orig.tar.xz dpkg-source: info: unpacking gmap_2024-11-20+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying install-data-local dpkg-source: info: applying remove_getopt_code_copy.patch dpkg-source: info: applying simd_fixes dpkg-source: info: applying c23.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2740700/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d85274bf58c74458a9c9761240c5f1a7' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2740700' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/pbuilderrc_sc0r --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b1 --logfile b1/build.log gmap_2024-11-20+ds-2.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2740700/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), architecture-is-little-endian, help2man, libbz2-dev, zlib1g-dev, debhelper, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 12.9 MB of archives. After unpacking 53.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get: 13 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 24 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 help2man amd64 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 12.9 MB in 0s (121 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package architecture-properties:amd64. Preparing to unpack .../11-architecture-properties_0.2.6_amd64.deb ... Unpacking architecture-properties:amd64 (0.2.6) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... 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Selecting previously unselected package libsimde-dev. Preparing to unpack .../33-libsimde-dev_0.8.2-3_all.deb ... Unpacking libsimde-dev (0.8.2-3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../34-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:amd64 (0.2.6) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gmap-2024-11-20+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gmap_2024-11-20+ds-2_source.changes dpkg-buildpackage: info: source package gmap dpkg-buildpackage: info: source version 2024-11-20+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --builddir build debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_clean --builddir build_avx512 dh_auto_clean --builddir build_avx2 dh_auto_clean --builddir build_sse42 dh_auto_clean --builddir build_sse41 dh_auto_clean --builddir build_ssse3 dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_autoreconf_clean -O--builddir=build dh_clean -O--builddir=build debian/rules binary dh binary --builddir build dh_update_autotools_config -O--builddir=build dh_autoreconf -O--builddir=build configure.ac:104: installing 'config/compile' configure.ac:85: installing 'config/config.guess' configure.ac:85: installing 'config/config.sub' configure.ac:109: installing 'config/install-sh' configure.ac:109: installing 'config/missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing 'config/depcomp' src/Makefile.am:870: warning: variable 'dist_compare2truth_SOURCES' is defined but no program or src/Makefile.am:870: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1216: warning: variable 'dist_gcount_bulk_SOURCES' is defined but no program or src/Makefile.am:1216: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1242: warning: variable 'dist_gcount_sc_SOURCES' is defined but no program or src/Makefile.am:1242: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:216: warning: variable 'dist_gexact_SOURCES' is defined but no program or src/Makefile.am:216: library has 'gexact' as canonical name (possible typo) src/Makefile.am:742: warning: variable 'dist_gexact_arm_SOURCES' is defined but no program or src/Makefile.am:742: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:772: warning: variable 'dist_gexact_avx2_SOURCES' is defined but no program or src/Makefile.am:772: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:778: warning: variable 'dist_gexact_avx512_SOURCES' is defined but no program or src/Makefile.am:778: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:784: warning: variable 'dist_gexact_avx512bw_SOURCES' is defined but no program or src/Makefile.am:784: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:736: warning: variable 'dist_gexact_nosimd_SOURCES' is defined but no program or src/Makefile.am:736: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:748: warning: variable 'dist_gexact_sse2_SOURCES' is defined but no program or src/Makefile.am:748: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:760: warning: variable 'dist_gexact_sse41_SOURCES' is defined but no program or src/Makefile.am:760: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:766: warning: variable 'dist_gexact_sse42_SOURCES' is defined but no program or src/Makefile.am:766: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:754: warning: variable 'dist_gexact_ssse3_SOURCES' is defined but no program or src/Makefile.am:754: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:223: warning: variable 'dist_gfilter_SOURCES' is defined but no program or src/Makefile.am:223: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:816: warning: variable 'dist_gfilter_arm_SOURCES' is defined but no program or src/Makefile.am:816: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:846: warning: variable 'dist_gfilter_avx2_SOURCES' is defined but no program or src/Makefile.am:846: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:852: warning: variable 'dist_gfilter_avx512_SOURCES' is defined but no program or src/Makefile.am:852: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:858: warning: variable 'dist_gfilter_avx512bw_SOURCES' is defined but no program or src/Makefile.am:858: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:810: warning: variable 'dist_gfilter_nosimd_SOURCES' is defined but no program or src/Makefile.am:810: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:822: warning: variable 'dist_gfilter_sse2_SOURCES' is defined but no program or src/Makefile.am:822: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:834: warning: variable 'dist_gfilter_sse41_SOURCES' is defined but no program or src/Makefile.am:834: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:840: warning: variable 'dist_gfilter_sse42_SOURCES' is defined but no program or src/Makefile.am:840: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:828: warning: variable 'dist_gfilter_ssse3_SOURCES' is defined but no program or src/Makefile.am:828: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1132: warning: variable 'dist_iit_pileup_SOURCES' is defined but no program or src/Makefile.am:1132: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1154: warning: variable 'dist_sam_sort_SOURCES' is defined but no program or src/Makefile.am:1154: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1172: warning: variable 'dist_umi_correct_SOURCES' is defined but no program or src/Makefile.am:1172: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1191: warning: variable 'dist_velocity_counts_SOURCES' is defined but no program or src/Makefile.am:1191: library has 'velocity_counts' as canonical name (possible typo) src/Makefile.am:869: warning: variable 'compare2truth_LDADD' is defined but no program or src/Makefile.am:869: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1215: warning: variable 'gcount_bulk_LDADD' is defined but no program or src/Makefile.am:1215: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1241: warning: variable 'gcount_sc_LDADD' is defined but no program or src/Makefile.am:1241: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:215: warning: variable 'gexact_LDADD' is defined but no program or src/Makefile.am:215: library has 'gexact' as canonical name (possible typo) src/Makefile.am:741: warning: variable 'gexact_arm_LDADD' is defined but no program or src/Makefile.am:741: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:771: warning: variable 'gexact_avx2_LDADD' is defined but no program or src/Makefile.am:771: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:777: warning: variable 'gexact_avx512_LDADD' is defined but no program or src/Makefile.am:777: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:783: warning: variable 'gexact_avx512bw_LDADD' is defined but no program or src/Makefile.am:783: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:735: warning: variable 'gexact_nosimd_LDADD' is defined but no program or src/Makefile.am:735: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:747: warning: variable 'gexact_sse2_LDADD' is defined but no program or src/Makefile.am:747: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:759: warning: variable 'gexact_sse41_LDADD' is defined but no program or src/Makefile.am:759: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:765: warning: variable 'gexact_sse42_LDADD' is defined but no program or src/Makefile.am:765: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:753: warning: variable 'gexact_ssse3_LDADD' is defined but no program or src/Makefile.am:753: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:222: warning: variable 'gfilter_LDADD' is defined but no program or src/Makefile.am:222: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:815: warning: variable 'gfilter_arm_LDADD' is defined but no program or src/Makefile.am:815: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:845: warning: variable 'gfilter_avx2_LDADD' is defined but no program or src/Makefile.am:845: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:851: warning: variable 'gfilter_avx512_LDADD' is defined but no program or src/Makefile.am:851: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:857: warning: variable 'gfilter_avx512bw_LDADD' is defined but no program or src/Makefile.am:857: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:809: warning: variable 'gfilter_nosimd_LDADD' is defined but no program or src/Makefile.am:809: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:821: warning: variable 'gfilter_sse2_LDADD' is defined but no program or src/Makefile.am:821: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:833: warning: variable 'gfilter_sse41_LDADD' is defined but no program or src/Makefile.am:833: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:839: warning: variable 'gfilter_sse42_LDADD' is defined but no program or src/Makefile.am:839: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:827: warning: variable 'gfilter_ssse3_LDADD' is defined but no program or src/Makefile.am:827: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1131: warning: variable 'iit_pileup_LDADD' is defined but no program or src/Makefile.am:1131: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1153: warning: variable 'sam_sort_LDADD' is defined but no program or src/Makefile.am:1153: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1171: warning: variable 'umi_correct_LDADD' is defined but no program or src/Makefile.am:1171: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1190: warning: variable 'velocity_counts_LDADD' is defined but no program or src/Makefile.am:1190: library has 'velocity_counts' as canonical name (possible typo) src/Makefile.am:868: warning: variable 'compare2truth_LDFLAGS' is defined but no program or src/Makefile.am:868: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1214: warning: variable 'gcount_bulk_LDFLAGS' is defined but no program or src/Makefile.am:1214: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1240: warning: variable 'gcount_sc_LDFLAGS' is defined but no program or src/Makefile.am:1240: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:214: warning: variable 'gexact_LDFLAGS' is defined but no program or src/Makefile.am:214: library has 'gexact' as canonical name (possible typo) src/Makefile.am:740: warning: variable 'gexact_arm_LDFLAGS' is defined but no program or src/Makefile.am:740: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:770: warning: variable 'gexact_avx2_LDFLAGS' is defined but no program or src/Makefile.am:770: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:776: warning: variable 'gexact_avx512_LDFLAGS' is defined but no program or src/Makefile.am:776: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:782: warning: variable 'gexact_avx512bw_LDFLAGS' is defined but no program or src/Makefile.am:782: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:734: warning: variable 'gexact_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:734: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:746: warning: variable 'gexact_sse2_LDFLAGS' is defined but no program or src/Makefile.am:746: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:758: warning: variable 'gexact_sse41_LDFLAGS' is defined but no program or src/Makefile.am:758: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:764: warning: variable 'gexact_sse42_LDFLAGS' is defined but no program or src/Makefile.am:764: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:752: warning: variable 'gexact_ssse3_LDFLAGS' is defined but no program or src/Makefile.am:752: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:221: warning: variable 'gfilter_LDFLAGS' is defined but no program or src/Makefile.am:221: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:814: warning: variable 'gfilter_arm_LDFLAGS' is defined but no program or src/Makefile.am:814: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:844: warning: variable 'gfilter_avx2_LDFLAGS' is defined but no program or src/Makefile.am:844: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:850: warning: variable 'gfilter_avx512_LDFLAGS' is defined but no program or src/Makefile.am:850: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:856: warning: variable 'gfilter_avx512bw_LDFLAGS' is defined but no program or src/Makefile.am:856: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:808: warning: variable 'gfilter_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:808: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:820: warning: variable 'gfilter_sse2_LDFLAGS' is defined but no program or src/Makefile.am:820: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:832: warning: variable 'gfilter_sse41_LDFLAGS' is defined but no program or src/Makefile.am:832: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:838: warning: variable 'gfilter_sse42_LDFLAGS' is defined but no program or src/Makefile.am:838: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:826: warning: variable 'gfilter_ssse3_LDFLAGS' is defined but no program or src/Makefile.am:826: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1130: warning: variable 'iit_pileup_LDFLAGS' is defined but no program or src/Makefile.am:1130: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1152: warning: variable 'sam_sort_LDFLAGS' is defined but no program or src/Makefile.am:1152: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1170: warning: variable 'umi_correct_LDFLAGS' is defined but no program or src/Makefile.am:1170: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1189: warning: variable 'velocity_counts_LDFLAGS' is defined but no program or src/Makefile.am:1189: library has 'velocity_counts' as canonical name (possible typo) parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' rm -Rf src/simde DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI" dh_auto_configure --reload-all-buildenv-variables -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2 cd build && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2 checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse2 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse2 checking SSE2 compiler flags to be used... -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI" dh_auto_configure --reload-all-buildenv-variables --builddir build_ssse3 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=ssse3 ax_cv_cpu_has_ssse3_ext=yes ax_cv_compile_ssse3_ext=yes ax_cv_link_tmmintrin_h=yes cd build_ssse3 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=ssse3 ax_cv_cpu_has_ssse3_ext=yes ax_cv_compile_ssse3_ext=yes ax_cv_link_tmmintrin_h=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... ssse3 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... ssse3 checking SSSE3 compiler flags to be used... -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_STTNI" dh_auto_configure --builddir build_sse41 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse41 ax_cv_cpu_has_sse41_ext=yes ax_cv_compile_sse41_ext=yes ax_cv_link_smmintrin_h=yes cd build_sse41 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse41 ax_cv_cpu_has_sse41_ext=yes ax_cv_compile_sse41_ext=yes ax_cv_link_smmintrin_h=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse41 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse41 checking SSE4.1 compiler flags to be used... -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 dh_auto_configure --builddir build_sse42 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse42 ax_cv_cpu_has_sse42_ext=yes ax_cv_compile_sse42_ext=yes ax_cv_link_nmmintrin_h=yes ax_cv_cpu_has_popcnt_ext=yes ax_make_sse42=yes ax_cv_cpu_has_bmi1_ext=yes ax_cv_compile_bmi_ext=yes ax_cv_link_bmi=yes cd build_sse42 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse42 ax_cv_cpu_has_sse42_ext=yes ax_cv_compile_sse42_ext=yes ax_cv_link_nmmintrin_h=yes ax_cv_cpu_has_popcnt_ext=yes ax_make_sse42=yes ax_cv_cpu_has_bmi1_ext=yes ax_cv_compile_bmi_ext=yes ax_cv_link_bmi=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm... yes checking for abm linker support... yes checking for _popcnt32 run support... yes checking for _lzcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi... yes checking for bmi linker support... yes checking for _tzcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse42 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse42 checking SSE4.2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 dh_auto_configure --builddir build_avx2 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx2 ax_make_avx2=yes ax_cv_cpu_has_bmi2_ext=yes ax_cv_compile_bmi2_ext=yes ax_cv_link_bmi2=yes cd build_avx2 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx2 ax_make_avx2=yes ax_cv_cpu_has_bmi2_ext=yes ax_cv_compile_bmi2_ext=yes ax_cv_link_bmi2=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2... yes checking for bmi2 linker support... yes checking for _pext run support... yes checking for user-selected SIMD level... avx2 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... avx2 checking AVX2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 dh_auto_configure --builddir build_avx512 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx512 ax_cv_cpu_has_avx512_ext=yes ax_cv_compile_avx512_ext=yes ax_cv_compile_avx512bw_ext=no ax_cv_link_avx512bw=no cd build_avx512 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx512 ax_cv_cpu_has_avx512_ext=yes ax_cv_compile_avx512_ext=yes ax_cv_compile_avx512bw_ext=no ax_cv_link_avx512bw=no checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd... yes checking for nmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw... yes checking for avx512vl and avx512bw linker support... yes checking for user-selected SIMD level... avx512 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... avx512 checking AVX512 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw # skipping avx512bw for now: # ../../src/oligoindex_hr.c: In function 'count_positions_fwd_simd': make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_build cd build && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read.c: In function 'IIT_debug': In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/iit-read-univ.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.sse2 gmap_sse2-except.o gmap_sse2-assert.o gmap_sse2-mem.o gmap_sse2-intlist.o gmap_sse2-uintlist.o gmap_sse2-list.o gmap_sse2-littleendian.o gmap_sse2-bigendian.o gmap_sse2-univinterval.o gmap_sse2-interval.o gmap_sse2-stopwatch.o gmap_sse2-semaphore.o gmap_sse2-access.o gmap_sse2-filestring.o gmap_sse2-iit-read-univ.o gmap_sse2-iit-read.o gmap_sse2-md5.o gmap_sse2-bzip2.o gmap_sse2-fopen.o gmap_sse2-sequence.o gmap_sse2-reader.o gmap_sse2-genomicpos.o gmap_sse2-compress.o gmap_sse2-compress-write.o gmap_sse2-gbuffer.o gmap_sse2-genome.o gmap_sse2-popcount.o gmap_sse2-dinucl_bits.o gmap_sse2-genome_canonical.o gmap_sse2-genome-write.o gmap_sse2-bitpack64-read.o gmap_sse2-bitpack64-readtwo.o gmap_sse2-indexdb.o gmap_sse2-oligo.o gmap_sse2-block.o gmap_sse2-chrom.o gmap_sse2-segmentpos.o gmap_sse2-chrnum.o gmap_sse2-uinttable_rh.o gmap_sse2-gregion.o gmap_sse2-match.o gmap_sse2-matchpool.o gmap_sse2-diagnostic.o gmap_sse2-stage1.o gmap_sse2-diag.o gmap_sse2-diagpool.o gmap_sse2-cmet.o gmap_sse2-atoi.o gmap_sse2-orderstat.o gmap_sse2-oligoindex_hr.o gmap_sse2-intron.o gmap_sse2-maxent.o gmap_sse2-maxent_hr.o gmap_sse2-pair.o gmap_sse2-pairpool.o gmap_sse2-cellpool.o gmap_sse2-stage2.o gmap_sse2-doublelist.o gmap_sse2-smooth.o gmap_sse2-splicestringpool.o gmap_sse2-splicetrie_build.o gmap_sse2-splicetrie.o gmap_sse2-boyer-moore.o gmap_sse2-dynprog.o gmap_sse2-dynprog_simd.o gmap_sse2-dynprog_single.o gmap_sse2-dynprog_genome.o gmap_sse2-dynprog_cdna.o gmap_sse2-dynprog_end.o gmap_sse2-translation.o gmap_sse2-pbinom.o gmap_sse2-changepoint.o gmap_sse2-stage3.o gmap_sse2-request.o gmap_sse2-result.o gmap_sse2-output.o gmap_sse2-inbuffer.o gmap_sse2-samheader.o gmap_sse2-printbuffer.o gmap_sse2-outbuffer.o gmap_sse2-chimera.o gmap_sse2-datadir.o gmap_sse2-parserange.o gmap_sse2-getline.o gmap_sse2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.sse2 gmapl_sse2-except.o gmapl_sse2-assert.o gmapl_sse2-mem.o gmapl_sse2-intlist.o gmapl_sse2-uintlist.o gmapl_sse2-uint8list.o gmapl_sse2-list.o gmapl_sse2-littleendian.o gmapl_sse2-bigendian.o gmapl_sse2-univinterval.o gmapl_sse2-interval.o gmapl_sse2-stopwatch.o gmapl_sse2-semaphore.o gmapl_sse2-access.o gmapl_sse2-filestring.o gmapl_sse2-iit-read-univ.o gmapl_sse2-iit-read.o gmapl_sse2-md5.o gmapl_sse2-bzip2.o gmapl_sse2-fopen.o gmapl_sse2-sequence.o gmapl_sse2-reader.o gmapl_sse2-genomicpos.o gmapl_sse2-compress.o gmapl_sse2-compress-write.o gmapl_sse2-gbuffer.o gmapl_sse2-genome.o gmapl_sse2-popcount.o gmapl_sse2-dinucl_bits.o gmapl_sse2-genome_canonical.o gmapl_sse2-genome-write.o gmapl_sse2-bitpack64-read.o gmapl_sse2-bitpack64-readtwo.o gmapl_sse2-indexdb.o gmapl_sse2-oligo.o gmapl_sse2-block.o gmapl_sse2-chrom.o gmapl_sse2-segmentpos.o gmapl_sse2-chrnum.o gmapl_sse2-uinttable_rh.o gmapl_sse2-uint8table_rh.o gmapl_sse2-gregion.o gmapl_sse2-match.o gmapl_sse2-matchpool.o gmapl_sse2-diagnostic.o gmapl_sse2-stage1.o gmapl_sse2-diag.o gmapl_sse2-diagpool.o gmapl_sse2-cmet.o gmapl_sse2-atoi.o gmapl_sse2-orderstat.o gmapl_sse2-oligoindex_hr.o gmapl_sse2-intron.o gmapl_sse2-maxent.o gmapl_sse2-maxent_hr.o gmapl_sse2-pair.o gmapl_sse2-pairpool.o gmapl_sse2-cellpool.o gmapl_sse2-stage2.o gmapl_sse2-doublelist.o gmapl_sse2-smooth.o gmapl_sse2-splicestringpool.o gmapl_sse2-splicetrie_build.o gmapl_sse2-splicetrie.o gmapl_sse2-boyer-moore.o gmapl_sse2-dynprog.o gmapl_sse2-dynprog_simd.o gmapl_sse2-dynprog_single.o gmapl_sse2-dynprog_genome.o gmapl_sse2-dynprog_cdna.o gmapl_sse2-dynprog_end.o gmapl_sse2-translation.o gmapl_sse2-pbinom.o gmapl_sse2-changepoint.o gmapl_sse2-stage3.o gmapl_sse2-request.o gmapl_sse2-result.o gmapl_sse2-output.o gmapl_sse2-inbuffer.o gmapl_sse2-samheader.o gmapl_sse2-printbuffer.o gmapl_sse2-outbuffer.o gmapl_sse2-chimera.o gmapl_sse2-datadir.o gmapl_sse2-parserange.o gmapl_sse2-getline.o gmapl_sse2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.sse2 gsnap_sse2-except.o gsnap_sse2-assert.o gsnap_sse2-mem.o gsnap_sse2-intlist.o gsnap_sse2-uintlist.o gsnap_sse2-list.o gsnap_sse2-littleendian.o gsnap_sse2-bigendian.o gsnap_sse2-univinterval.o gsnap_sse2-interval.o gsnap_sse2-stopwatch.o gsnap_sse2-semaphore.o gsnap_sse2-access.o gsnap_sse2-filestring.o gsnap_sse2-iit-read-univ.o gsnap_sse2-iit-read.o gsnap_sse2-bzip2.o gsnap_sse2-reader.o gsnap_sse2-genomicpos.o gsnap_sse2-compress.o gsnap_sse2-genome.o gsnap_sse2-transcriptome.o gsnap_sse2-popcount.o gsnap_sse2-genomebits.o gsnap_sse2-genomebits_consec.o gsnap_sse2-genomebits_count.o gsnap_sse2-genomebits_kmer.o gsnap_sse2-genomebits_indel.o gsnap_sse2-genomebits_decode.o gsnap_sse2-genomebits_mismatches.o gsnap_sse2-genomebits_trim.o gsnap_sse2-dinucl_bits.o gsnap_sse2-genome_sites.o gsnap_sse2-bitpack64-read.o gsnap_sse2-bitpack64-readtwo.o gsnap_sse2-mergeinfo.o gsnap_sse2-merge-diagonals-heap-uint4.o gsnap_sse2-merge-uint4.o gsnap_sse2-merge-diagonals-simd-uint4.o gsnap_sse2-indexdb.o gsnap_sse2-localdb-read.o gsnap_sse2-oligo.o gsnap_sse2-chrnum.o gsnap_sse2-maxent_hr.o gsnap_sse2-mapq.o gsnap_sse2-fopen.o gsnap_sse2-shortread.o gsnap_sse2-junction.o gsnap_sse2-concordance.o gsnap_sse2-simplepair.o gsnap_sse2-orderstat.o gsnap_sse2-intlistpool.o gsnap_sse2-uintlistpool.o gsnap_sse2-listpool.o gsnap_sse2-hitlistpool.o gsnap_sse2-pathpool.o gsnap_sse2-auxinfopool.o gsnap_sse2-pathstorepool.o gsnap_sse2-intron.o gsnap_sse2-gbuffer.o gsnap_sse2-select64-common.o gsnap_sse2-select64-ones.o gsnap_sse2-select64-zeroes.o gsnap_sse2-ef64.o gsnap_sse2-nr-x.o gsnap_sse2-knownsplicing.o gsnap_sse2-knownindels.o gsnap_sse2-splice.o gsnap_sse2-indel.o gsnap_sse2-spliceendsgen.o gsnap_sse2-spliceends.o gsnap_sse2-bitpack64-access.o gsnap_sse2-trdiag.o gsnap_sse2-trdiagpool.o gsnap_sse2-tr-extension-search.o gsnap_sse2-univdiag.o gsnap_sse2-univdiagpool.o gsnap_sse2-sedgesort.o gsnap_sse2-auxinfo.o gsnap_sse2-pathstore.o gsnap_sse2-altsplice.o gsnap_sse2-path.o gsnap_sse2-pathpair.o gsnap_sse2-path-solve.o gsnap_sse2-path-fusion.o gsnap_sse2-path-trim.o gsnap_sse2-path-eval.o gsnap_sse2-pathpair-eval.o gsnap_sse2-path-print-alignment.o gsnap_sse2-path-print-m8.o gsnap_sse2-path-print-sam.o gsnap_sse2-path-learn.o gsnap_sse2-method.o gsnap_sse2-doublelist.o gsnap_sse2-bitvector.o gsnap_sse2-transcriptpool.o gsnap_sse2-exon.o gsnap_sse2-transcript.o gsnap_sse2-trpathpool.o gsnap_sse2-trpath.o gsnap_sse2-trpath-solve.o gsnap_sse2-trpath-convert.o gsnap_sse2-trpath-eval.o gsnap_sse2-transcriptome-search.o gsnap_sse2-vectorpool.o gsnap_sse2-repair.o gsnap_sse2-transcript-remap.o gsnap_sse2-transcript-velocity.o gsnap_sse2-intersect-small.o gsnap_sse2-intersect-uint2.o gsnap_sse2-intersect-approx-uint4.o gsnap_sse2-intersect-approx-indices-uint4.o gsnap_sse2-intersect-wdups-indices.o gsnap_sse2-intersect-lower-small.o gsnap_sse2-intersect-higher-small.o gsnap_sse2-intersect-indices-small.o gsnap_sse2-intersect-indices2-small.o gsnap_sse2-intersect-concordance-uint4.o gsnap_sse2-kmer-search.o gsnap_sse2-extension-search.o gsnap_sse2-repetitive.o gsnap_sse2-uint8table.o gsnap_sse2-uinttable.o gsnap_sse2-stage1hr.o gsnap_sse2-stage1hr-single.o gsnap_sse2-stage1hr-paired.o gsnap_sse2-uinttableuint.o gsnap_sse2-tableuint.o gsnap_sse2-single-cell.o gsnap_sse2-request.o gsnap_sse2-resulthr.o gsnap_sse2-output.o gsnap_sse2-inbuffer.o gsnap_sse2-samheader.o gsnap_sse2-printbuffer.o gsnap_sse2-outbuffer.o gsnap_sse2-uintpairtable.o gsnap_sse2-splice-count.o gsnap_sse2-support.o gsnap_sse2-datadir.o gsnap_sse2-parserange.o gsnap_sse2-getline.o gsnap_sse2-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.sse2 gsnapl_sse2-except.o gsnapl_sse2-assert.o gsnapl_sse2-mem.o gsnapl_sse2-intlist.o gsnapl_sse2-uintlist.o gsnapl_sse2-uint8list.o gsnapl_sse2-list.o gsnapl_sse2-littleendian.o gsnapl_sse2-bigendian.o gsnapl_sse2-univinterval.o gsnapl_sse2-interval.o gsnapl_sse2-stopwatch.o gsnapl_sse2-semaphore.o gsnapl_sse2-access.o gsnapl_sse2-filestring.o gsnapl_sse2-iit-read-univ.o gsnapl_sse2-iit-read.o gsnapl_sse2-bzip2.o gsnapl_sse2-reader.o gsnapl_sse2-genomicpos.o gsnapl_sse2-compress.o gsnapl_sse2-genome.o gsnapl_sse2-transcriptome.o gsnapl_sse2-popcount.o gsnapl_sse2-genomebits.o gsnapl_sse2-genomebits_consec.o gsnapl_sse2-genomebits_count.o gsnapl_sse2-genomebits_kmer.o gsnapl_sse2-genomebits_indel.o gsnapl_sse2-genomebits_decode.o gsnapl_sse2-genomebits_mismatches.o gsnapl_sse2-genomebits_trim.o gsnapl_sse2-dinucl_bits.o gsnapl_sse2-genome_sites.o gsnapl_sse2-bitpack64-read.o gsnapl_sse2-bitpack64-readtwo.o gsnapl_sse2-mergeinfo.o gsnapl_sse2-merge-diagonals-heap-uint8.o gsnapl_sse2-merge-uint8.o gsnapl_sse2-merge-diagonals-simd-uint8.o gsnapl_sse2-merge-diagonals-heap-uint4.o gsnapl_sse2-merge-uint4.o gsnapl_sse2-merge-diagonals-simd-uint4.o gsnapl_sse2-indexdb.o gsnapl_sse2-localdb-read.o gsnapl_sse2-oligo.o gsnapl_sse2-chrnum.o gsnapl_sse2-maxent_hr.o gsnapl_sse2-mapq.o gsnapl_sse2-fopen.o gsnapl_sse2-shortread.o gsnapl_sse2-junction.o gsnapl_sse2-concordance.o gsnapl_sse2-simplepair.o gsnapl_sse2-orderstat.o gsnapl_sse2-intlistpool.o gsnapl_sse2-uintlistpool.o gsnapl_sse2-uint8listpool.o gsnapl_sse2-listpool.o gsnapl_sse2-hitlistpool.o gsnapl_sse2-pathpool.o gsnapl_sse2-auxinfopool.o gsnapl_sse2-pathstorepool.o gsnapl_sse2-intron.o gsnapl_sse2-gbuffer.o gsnapl_sse2-select64-common.o gsnapl_sse2-select64-ones.o gsnapl_sse2-select64-zeroes.o gsnapl_sse2-ef64.o gsnapl_sse2-nr-x.o gsnapl_sse2-knownsplicing.o gsnapl_sse2-knownindels.o gsnapl_sse2-splice.o gsnapl_sse2-indel.o gsnapl_sse2-spliceendsgen.o gsnapl_sse2-spliceends.o gsnapl_sse2-bitpack64-access.o gsnapl_sse2-trdiag.o gsnapl_sse2-trdiagpool.o gsnapl_sse2-tr-extension-search.o gsnapl_sse2-univdiag.o gsnapl_sse2-univdiagpool.o gsnapl_sse2-sedgesort.o gsnapl_sse2-auxinfo.o gsnapl_sse2-pathstore.o gsnapl_sse2-altsplice.o gsnapl_sse2-path.o gsnapl_sse2-pathpair.o gsnapl_sse2-path-solve.o gsnapl_sse2-path-fusion.o gsnapl_sse2-path-trim.o gsnapl_sse2-path-eval.o gsnapl_sse2-pathpair-eval.o gsnapl_sse2-path-print-alignment.o gsnapl_sse2-path-print-m8.o gsnapl_sse2-path-print-sam.o gsnapl_sse2-path-learn.o gsnapl_sse2-method.o gsnapl_sse2-doublelist.o gsnapl_sse2-bitvector.o gsnapl_sse2-transcriptpool.o gsnapl_sse2-exon.o gsnapl_sse2-transcript.o gsnapl_sse2-trpathpool.o gsnapl_sse2-trpath.o gsnapl_sse2-trpath-solve.o gsnapl_sse2-trpath-convert.o gsnapl_sse2-trpath-eval.o gsnapl_sse2-transcriptome-search.o gsnapl_sse2-vectorpool.o gsnapl_sse2-repair.o gsnapl_sse2-transcript-remap.o gsnapl_sse2-transcript-velocity.o gsnapl_sse2-intersect-large.o gsnapl_sse2-intersect-small.o gsnapl_sse2-intersect-uint2.o gsnapl_sse2-intersect-approx-uint4.o gsnapl_sse2-intersect-approx-uint8.o gsnapl_sse2-intersect-approx-indices-uint8.o gsnapl_sse2-intersect-wdups-indices.o gsnapl_sse2-intersect-lower-large.o gsnapl_sse2-intersect-higher-large.o gsnapl_sse2-intersect-indices-small.o gsnapl_sse2-intersect-indices2-large.o gsnapl_sse2-intersect-indices-uint8.o gsnapl_sse2-intersect-concordance-uint8.o gsnapl_sse2-kmer-search.o gsnapl_sse2-extension-search.o gsnapl_sse2-repetitive.o gsnapl_sse2-uint8table.o gsnapl_sse2-stage1hr.o gsnapl_sse2-stage1hr-single.o gsnapl_sse2-stage1hr-paired.o gsnapl_sse2-uint8tableuint.o gsnapl_sse2-tableuint.o gsnapl_sse2-single-cell.o gsnapl_sse2-request.o gsnapl_sse2-resulthr.o gsnapl_sse2-output.o gsnapl_sse2-inbuffer.o gsnapl_sse2-samheader.o gsnapl_sse2-printbuffer.o gsnapl_sse2-outbuffer.o gsnapl_sse2-uint8pairtable.o gsnapl_sse2-splice-count.o gsnapl_sse2-support.o gsnapl_sse2-datadir.o gsnapl_sse2-parserange.o gsnapl_sse2-getline.o gsnapl_sse2-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes chmod +x md_coords chmod +x fa_coords chmod +x psl_splicesites chmod +x psl_introns chmod +x psl_genes chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_splicesites cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_introns chmod +x gtf_genes chmod +x gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x gff3_introns chmod +x gff3_genes chmod +x dbsnp_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' dh_auto_build --builddir build_ssse3 cd build_ssse3 && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.ssse3 gmap_ssse3-except.o gmap_ssse3-assert.o gmap_ssse3-mem.o gmap_ssse3-intlist.o gmap_ssse3-uintlist.o gmap_ssse3-list.o gmap_ssse3-littleendian.o gmap_ssse3-bigendian.o gmap_ssse3-univinterval.o gmap_ssse3-interval.o gmap_ssse3-stopwatch.o gmap_ssse3-semaphore.o gmap_ssse3-access.o gmap_ssse3-filestring.o gmap_ssse3-iit-read-univ.o gmap_ssse3-iit-read.o gmap_ssse3-md5.o gmap_ssse3-bzip2.o gmap_ssse3-fopen.o gmap_ssse3-sequence.o gmap_ssse3-reader.o gmap_ssse3-genomicpos.o gmap_ssse3-compress.o gmap_ssse3-compress-write.o gmap_ssse3-gbuffer.o gmap_ssse3-genome.o gmap_ssse3-popcount.o gmap_ssse3-dinucl_bits.o gmap_ssse3-genome_canonical.o gmap_ssse3-genome-write.o gmap_ssse3-bitpack64-read.o gmap_ssse3-bitpack64-readtwo.o gmap_ssse3-indexdb.o gmap_ssse3-oligo.o gmap_ssse3-block.o gmap_ssse3-chrom.o gmap_ssse3-segmentpos.o gmap_ssse3-chrnum.o gmap_ssse3-uinttable_rh.o gmap_ssse3-gregion.o gmap_ssse3-match.o gmap_ssse3-matchpool.o gmap_ssse3-diagnostic.o gmap_ssse3-stage1.o gmap_ssse3-diag.o gmap_ssse3-diagpool.o gmap_ssse3-cmet.o gmap_ssse3-atoi.o gmap_ssse3-orderstat.o gmap_ssse3-oligoindex_hr.o gmap_ssse3-intron.o gmap_ssse3-maxent.o gmap_ssse3-maxent_hr.o gmap_ssse3-pair.o gmap_ssse3-pairpool.o gmap_ssse3-cellpool.o gmap_ssse3-stage2.o gmap_ssse3-doublelist.o gmap_ssse3-smooth.o gmap_ssse3-splicestringpool.o gmap_ssse3-splicetrie_build.o gmap_ssse3-splicetrie.o gmap_ssse3-boyer-moore.o gmap_ssse3-dynprog.o gmap_ssse3-dynprog_simd.o gmap_ssse3-dynprog_single.o gmap_ssse3-dynprog_genome.o gmap_ssse3-dynprog_cdna.o gmap_ssse3-dynprog_end.o gmap_ssse3-translation.o gmap_ssse3-pbinom.o gmap_ssse3-changepoint.o gmap_ssse3-stage3.o gmap_ssse3-request.o gmap_ssse3-result.o gmap_ssse3-output.o gmap_ssse3-inbuffer.o gmap_ssse3-samheader.o gmap_ssse3-printbuffer.o gmap_ssse3-outbuffer.o gmap_ssse3-chimera.o gmap_ssse3-datadir.o gmap_ssse3-parserange.o gmap_ssse3-getline.o gmap_ssse3-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.ssse3 gsnap_ssse3-except.o gsnap_ssse3-assert.o gsnap_ssse3-mem.o gsnap_ssse3-intlist.o gsnap_ssse3-uintlist.o gsnap_ssse3-list.o gsnap_ssse3-littleendian.o gsnap_ssse3-bigendian.o gsnap_ssse3-univinterval.o gsnap_ssse3-interval.o gsnap_ssse3-stopwatch.o gsnap_ssse3-semaphore.o gsnap_ssse3-access.o gsnap_ssse3-filestring.o gsnap_ssse3-iit-read-univ.o gsnap_ssse3-iit-read.o gsnap_ssse3-bzip2.o gsnap_ssse3-reader.o gsnap_ssse3-genomicpos.o gsnap_ssse3-compress.o gsnap_ssse3-genome.o gsnap_ssse3-transcriptome.o gsnap_ssse3-popcount.o gsnap_ssse3-genomebits.o gsnap_ssse3-genomebits_consec.o gsnap_ssse3-genomebits_count.o gsnap_ssse3-genomebits_kmer.o gsnap_ssse3-genomebits_indel.o gsnap_ssse3-genomebits_decode.o gsnap_ssse3-genomebits_mismatches.o gsnap_ssse3-genomebits_trim.o gsnap_ssse3-dinucl_bits.o gsnap_ssse3-genome_sites.o gsnap_ssse3-bitpack64-read.o gsnap_ssse3-bitpack64-readtwo.o gsnap_ssse3-mergeinfo.o gsnap_ssse3-merge-diagonals-heap-uint4.o gsnap_ssse3-merge-uint4.o gsnap_ssse3-merge-diagonals-simd-uint4.o gsnap_ssse3-indexdb.o gsnap_ssse3-localdb-read.o gsnap_ssse3-oligo.o gsnap_ssse3-chrnum.o gsnap_ssse3-maxent_hr.o gsnap_ssse3-mapq.o gsnap_ssse3-fopen.o gsnap_ssse3-shortread.o gsnap_ssse3-junction.o gsnap_ssse3-concordance.o gsnap_ssse3-simplepair.o gsnap_ssse3-orderstat.o gsnap_ssse3-intlistpool.o gsnap_ssse3-uintlistpool.o gsnap_ssse3-listpool.o gsnap_ssse3-hitlistpool.o gsnap_ssse3-pathpool.o gsnap_ssse3-auxinfopool.o gsnap_ssse3-pathstorepool.o gsnap_ssse3-intron.o gsnap_ssse3-gbuffer.o gsnap_ssse3-select64-common.o gsnap_ssse3-select64-ones.o gsnap_ssse3-select64-zeroes.o gsnap_ssse3-ef64.o gsnap_ssse3-nr-x.o gsnap_ssse3-knownsplicing.o gsnap_ssse3-knownindels.o gsnap_ssse3-splice.o gsnap_ssse3-indel.o gsnap_ssse3-spliceendsgen.o gsnap_ssse3-spliceends.o gsnap_ssse3-bitpack64-access.o gsnap_ssse3-trdiag.o gsnap_ssse3-trdiagpool.o gsnap_ssse3-tr-extension-search.o gsnap_ssse3-univdiag.o gsnap_ssse3-univdiagpool.o gsnap_ssse3-sedgesort.o gsnap_ssse3-auxinfo.o gsnap_ssse3-pathstore.o gsnap_ssse3-altsplice.o gsnap_ssse3-path.o gsnap_ssse3-pathpair.o gsnap_ssse3-path-solve.o gsnap_ssse3-path-fusion.o gsnap_ssse3-path-trim.o gsnap_ssse3-path-eval.o gsnap_ssse3-pathpair-eval.o gsnap_ssse3-path-print-alignment.o gsnap_ssse3-path-print-m8.o gsnap_ssse3-path-print-sam.o gsnap_ssse3-path-learn.o gsnap_ssse3-method.o gsnap_ssse3-doublelist.o gsnap_ssse3-bitvector.o gsnap_ssse3-transcriptpool.o gsnap_ssse3-exon.o gsnap_ssse3-transcript.o gsnap_ssse3-trpathpool.o gsnap_ssse3-trpath.o gsnap_ssse3-trpath-solve.o gsnap_ssse3-trpath-convert.o gsnap_ssse3-trpath-eval.o gsnap_ssse3-transcriptome-search.o gsnap_ssse3-vectorpool.o gsnap_ssse3-repair.o gsnap_ssse3-transcript-remap.o gsnap_ssse3-transcript-velocity.o gsnap_ssse3-intersect-small.o gsnap_ssse3-intersect-uint2.o gsnap_ssse3-intersect-approx-uint4.o gsnap_ssse3-intersect-approx-indices-uint4.o gsnap_ssse3-intersect-wdups-indices.o gsnap_ssse3-intersect-lower-small.o gsnap_ssse3-intersect-higher-small.o gsnap_ssse3-intersect-indices-small.o gsnap_ssse3-intersect-indices2-small.o gsnap_ssse3-intersect-concordance-uint4.o gsnap_ssse3-kmer-search.o gsnap_ssse3-extension-search.o gsnap_ssse3-repetitive.o gsnap_ssse3-uint8table.o gsnap_ssse3-uinttable.o gsnap_ssse3-stage1hr.o gsnap_ssse3-stage1hr-single.o gsnap_ssse3-stage1hr-paired.o gsnap_ssse3-uinttableuint.o gsnap_ssse3-tableuint.o gsnap_ssse3-single-cell.o gsnap_ssse3-request.o gsnap_ssse3-resulthr.o gsnap_ssse3-output.o gsnap_ssse3-inbuffer.o gsnap_ssse3-samheader.o gsnap_ssse3-printbuffer.o gsnap_ssse3-outbuffer.o gsnap_ssse3-uintpairtable.o gsnap_ssse3-splice-count.o gsnap_ssse3-support.o gsnap_ssse3-datadir.o gsnap_ssse3-parserange.o gsnap_ssse3-getline.o gsnap_ssse3-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.ssse3 gmapl_ssse3-except.o gmapl_ssse3-assert.o gmapl_ssse3-mem.o gmapl_ssse3-intlist.o gmapl_ssse3-uintlist.o gmapl_ssse3-uint8list.o gmapl_ssse3-list.o gmapl_ssse3-littleendian.o gmapl_ssse3-bigendian.o gmapl_ssse3-univinterval.o gmapl_ssse3-interval.o gmapl_ssse3-stopwatch.o gmapl_ssse3-semaphore.o gmapl_ssse3-access.o gmapl_ssse3-filestring.o gmapl_ssse3-iit-read-univ.o gmapl_ssse3-iit-read.o gmapl_ssse3-md5.o gmapl_ssse3-bzip2.o gmapl_ssse3-fopen.o gmapl_ssse3-sequence.o gmapl_ssse3-reader.o gmapl_ssse3-genomicpos.o gmapl_ssse3-compress.o gmapl_ssse3-compress-write.o gmapl_ssse3-gbuffer.o gmapl_ssse3-genome.o gmapl_ssse3-popcount.o gmapl_ssse3-dinucl_bits.o gmapl_ssse3-genome_canonical.o gmapl_ssse3-genome-write.o gmapl_ssse3-bitpack64-read.o gmapl_ssse3-bitpack64-readtwo.o gmapl_ssse3-indexdb.o gmapl_ssse3-oligo.o gmapl_ssse3-block.o gmapl_ssse3-chrom.o gmapl_ssse3-segmentpos.o gmapl_ssse3-chrnum.o gmapl_ssse3-uinttable_rh.o gmapl_ssse3-uint8table_rh.o gmapl_ssse3-gregion.o gmapl_ssse3-match.o gmapl_ssse3-matchpool.o gmapl_ssse3-diagnostic.o gmapl_ssse3-stage1.o gmapl_ssse3-diag.o gmapl_ssse3-diagpool.o gmapl_ssse3-cmet.o gmapl_ssse3-atoi.o gmapl_ssse3-orderstat.o gmapl_ssse3-oligoindex_hr.o gmapl_ssse3-intron.o gmapl_ssse3-maxent.o gmapl_ssse3-maxent_hr.o gmapl_ssse3-pair.o gmapl_ssse3-pairpool.o gmapl_ssse3-cellpool.o gmapl_ssse3-stage2.o gmapl_ssse3-doublelist.o gmapl_ssse3-smooth.o gmapl_ssse3-splicestringpool.o gmapl_ssse3-splicetrie_build.o gmapl_ssse3-splicetrie.o gmapl_ssse3-boyer-moore.o gmapl_ssse3-dynprog.o gmapl_ssse3-dynprog_simd.o gmapl_ssse3-dynprog_single.o gmapl_ssse3-dynprog_genome.o gmapl_ssse3-dynprog_cdna.o gmapl_ssse3-dynprog_end.o gmapl_ssse3-translation.o gmapl_ssse3-pbinom.o gmapl_ssse3-changepoint.o gmapl_ssse3-stage3.o gmapl_ssse3-request.o gmapl_ssse3-result.o gmapl_ssse3-output.o gmapl_ssse3-inbuffer.o gmapl_ssse3-samheader.o gmapl_ssse3-printbuffer.o gmapl_ssse3-outbuffer.o gmapl_ssse3-chimera.o gmapl_ssse3-datadir.o gmapl_ssse3-parserange.o gmapl_ssse3-getline.o gmapl_ssse3-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.ssse3 gsnapl_ssse3-except.o gsnapl_ssse3-assert.o gsnapl_ssse3-mem.o gsnapl_ssse3-intlist.o gsnapl_ssse3-uintlist.o gsnapl_ssse3-uint8list.o gsnapl_ssse3-list.o gsnapl_ssse3-littleendian.o gsnapl_ssse3-bigendian.o gsnapl_ssse3-univinterval.o gsnapl_ssse3-interval.o gsnapl_ssse3-stopwatch.o gsnapl_ssse3-semaphore.o gsnapl_ssse3-access.o gsnapl_ssse3-filestring.o gsnapl_ssse3-iit-read-univ.o gsnapl_ssse3-iit-read.o gsnapl_ssse3-bzip2.o gsnapl_ssse3-reader.o gsnapl_ssse3-genomicpos.o gsnapl_ssse3-compress.o gsnapl_ssse3-genome.o gsnapl_ssse3-transcriptome.o gsnapl_ssse3-popcount.o gsnapl_ssse3-genomebits.o gsnapl_ssse3-genomebits_consec.o gsnapl_ssse3-genomebits_count.o gsnapl_ssse3-genomebits_kmer.o gsnapl_ssse3-genomebits_indel.o gsnapl_ssse3-genomebits_decode.o gsnapl_ssse3-genomebits_mismatches.o gsnapl_ssse3-genomebits_trim.o gsnapl_ssse3-dinucl_bits.o gsnapl_ssse3-genome_sites.o gsnapl_ssse3-bitpack64-read.o gsnapl_ssse3-bitpack64-readtwo.o gsnapl_ssse3-mergeinfo.o gsnapl_ssse3-merge-diagonals-heap-uint8.o gsnapl_ssse3-merge-uint8.o gsnapl_ssse3-merge-diagonals-simd-uint8.o gsnapl_ssse3-merge-diagonals-heap-uint4.o gsnapl_ssse3-merge-uint4.o gsnapl_ssse3-merge-diagonals-simd-uint4.o gsnapl_ssse3-indexdb.o gsnapl_ssse3-localdb-read.o gsnapl_ssse3-oligo.o gsnapl_ssse3-chrnum.o gsnapl_ssse3-maxent_hr.o gsnapl_ssse3-mapq.o gsnapl_ssse3-fopen.o gsnapl_ssse3-shortread.o gsnapl_ssse3-junction.o gsnapl_ssse3-concordance.o gsnapl_ssse3-simplepair.o gsnapl_ssse3-orderstat.o gsnapl_ssse3-intlistpool.o gsnapl_ssse3-uintlistpool.o gsnapl_ssse3-uint8listpool.o gsnapl_ssse3-listpool.o gsnapl_ssse3-hitlistpool.o gsnapl_ssse3-pathpool.o gsnapl_ssse3-auxinfopool.o gsnapl_ssse3-pathstorepool.o gsnapl_ssse3-intron.o gsnapl_ssse3-gbuffer.o gsnapl_ssse3-select64-common.o gsnapl_ssse3-select64-ones.o gsnapl_ssse3-select64-zeroes.o gsnapl_ssse3-ef64.o gsnapl_ssse3-nr-x.o gsnapl_ssse3-knownsplicing.o gsnapl_ssse3-knownindels.o gsnapl_ssse3-splice.o gsnapl_ssse3-indel.o gsnapl_ssse3-spliceendsgen.o gsnapl_ssse3-spliceends.o gsnapl_ssse3-bitpack64-access.o gsnapl_ssse3-trdiag.o gsnapl_ssse3-trdiagpool.o gsnapl_ssse3-tr-extension-search.o gsnapl_ssse3-univdiag.o gsnapl_ssse3-univdiagpool.o gsnapl_ssse3-sedgesort.o gsnapl_ssse3-auxinfo.o gsnapl_ssse3-pathstore.o gsnapl_ssse3-altsplice.o gsnapl_ssse3-path.o gsnapl_ssse3-pathpair.o gsnapl_ssse3-path-solve.o gsnapl_ssse3-path-fusion.o gsnapl_ssse3-path-trim.o gsnapl_ssse3-path-eval.o gsnapl_ssse3-pathpair-eval.o gsnapl_ssse3-path-print-alignment.o gsnapl_ssse3-path-print-m8.o gsnapl_ssse3-path-print-sam.o gsnapl_ssse3-path-learn.o gsnapl_ssse3-method.o gsnapl_ssse3-doublelist.o gsnapl_ssse3-bitvector.o gsnapl_ssse3-transcriptpool.o gsnapl_ssse3-exon.o gsnapl_ssse3-transcript.o gsnapl_ssse3-trpathpool.o gsnapl_ssse3-trpath.o gsnapl_ssse3-trpath-solve.o gsnapl_ssse3-trpath-convert.o gsnapl_ssse3-trpath-eval.o gsnapl_ssse3-transcriptome-search.o gsnapl_ssse3-vectorpool.o gsnapl_ssse3-repair.o gsnapl_ssse3-transcript-remap.o gsnapl_ssse3-transcript-velocity.o gsnapl_ssse3-intersect-large.o gsnapl_ssse3-intersect-small.o gsnapl_ssse3-intersect-uint2.o gsnapl_ssse3-intersect-approx-uint4.o gsnapl_ssse3-intersect-approx-uint8.o gsnapl_ssse3-intersect-approx-indices-uint8.o gsnapl_ssse3-intersect-wdups-indices.o gsnapl_ssse3-intersect-lower-large.o gsnapl_ssse3-intersect-higher-large.o gsnapl_ssse3-intersect-indices-small.o gsnapl_ssse3-intersect-indices2-large.o gsnapl_ssse3-intersect-indices-uint8.o gsnapl_ssse3-intersect-concordance-uint8.o gsnapl_ssse3-kmer-search.o gsnapl_ssse3-extension-search.o gsnapl_ssse3-repetitive.o gsnapl_ssse3-uint8table.o gsnapl_ssse3-stage1hr.o gsnapl_ssse3-stage1hr-single.o gsnapl_ssse3-stage1hr-paired.o gsnapl_ssse3-uint8tableuint.o gsnapl_ssse3-tableuint.o gsnapl_ssse3-single-cell.o gsnapl_ssse3-request.o gsnapl_ssse3-resulthr.o gsnapl_ssse3-output.o gsnapl_ssse3-inbuffer.o gsnapl_ssse3-samheader.o gsnapl_ssse3-printbuffer.o gsnapl_ssse3-outbuffer.o gsnapl_ssse3-uint8pairtable.o gsnapl_ssse3-splice-count.o gsnapl_ssse3-support.o gsnapl_ssse3-datadir.o gsnapl_ssse3-parserange.o gsnapl_ssse3-getline.o gsnapl_ssse3-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns chmod +x fa_coords chmod +x md_coords chmod +x psl_splicesites chmod +x psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x psl_genes cp gtf_genes.pl gtf_genes chmod +x ensembl_genes chmod +x gtf_splicesites chmod +x gtf_introns cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes chmod +x gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_introns chmod +x gff3_genes chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' dh_auto_build --builddir build_sse41 cd build_sse41 && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read.c: In function 'IIT_read': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c: In function 'IIT_read': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse41 gmapl_sse41-except.o gmapl_sse41-assert.o gmapl_sse41-mem.o gmapl_sse41-intlist.o gmapl_sse41-uintlist.o gmapl_sse41-uint8list.o gmapl_sse41-list.o gmapl_sse41-littleendian.o gmapl_sse41-bigendian.o gmapl_sse41-univinterval.o gmapl_sse41-interval.o gmapl_sse41-stopwatch.o gmapl_sse41-semaphore.o gmapl_sse41-access.o gmapl_sse41-filestring.o gmapl_sse41-iit-read-univ.o gmapl_sse41-iit-read.o gmapl_sse41-md5.o gmapl_sse41-bzip2.o gmapl_sse41-fopen.o gmapl_sse41-sequence.o gmapl_sse41-reader.o gmapl_sse41-genomicpos.o gmapl_sse41-compress.o gmapl_sse41-compress-write.o gmapl_sse41-gbuffer.o gmapl_sse41-genome.o gmapl_sse41-popcount.o gmapl_sse41-dinucl_bits.o gmapl_sse41-genome_canonical.o gmapl_sse41-genome-write.o gmapl_sse41-bitpack64-read.o gmapl_sse41-bitpack64-readtwo.o gmapl_sse41-indexdb.o gmapl_sse41-oligo.o gmapl_sse41-block.o gmapl_sse41-chrom.o gmapl_sse41-segmentpos.o gmapl_sse41-chrnum.o gmapl_sse41-uinttable_rh.o gmapl_sse41-uint8table_rh.o gmapl_sse41-gregion.o gmapl_sse41-match.o gmapl_sse41-matchpool.o gmapl_sse41-diagnostic.o gmapl_sse41-stage1.o gmapl_sse41-diag.o gmapl_sse41-diagpool.o gmapl_sse41-cmet.o gmapl_sse41-atoi.o gmapl_sse41-orderstat.o gmapl_sse41-oligoindex_hr.o gmapl_sse41-intron.o gmapl_sse41-maxent.o gmapl_sse41-maxent_hr.o gmapl_sse41-pair.o gmapl_sse41-pairpool.o gmapl_sse41-cellpool.o gmapl_sse41-stage2.o gmapl_sse41-doublelist.o gmapl_sse41-smooth.o gmapl_sse41-splicestringpool.o gmapl_sse41-splicetrie_build.o gmapl_sse41-splicetrie.o gmapl_sse41-boyer-moore.o gmapl_sse41-dynprog.o gmapl_sse41-dynprog_simd.o gmapl_sse41-dynprog_single.o gmapl_sse41-dynprog_genome.o gmapl_sse41-dynprog_cdna.o gmapl_sse41-dynprog_end.o gmapl_sse41-translation.o gmapl_sse41-pbinom.o gmapl_sse41-changepoint.o gmapl_sse41-stage3.o gmapl_sse41-request.o gmapl_sse41-result.o gmapl_sse41-output.o gmapl_sse41-inbuffer.o gmapl_sse41-samheader.o gmapl_sse41-printbuffer.o gmapl_sse41-outbuffer.o gmapl_sse41-chimera.o gmapl_sse41-datadir.o gmapl_sse41-parserange.o gmapl_sse41-getline.o gmapl_sse41-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse41 gmap_sse41-except.o gmap_sse41-assert.o gmap_sse41-mem.o gmap_sse41-intlist.o gmap_sse41-uintlist.o gmap_sse41-list.o gmap_sse41-littleendian.o gmap_sse41-bigendian.o gmap_sse41-univinterval.o gmap_sse41-interval.o gmap_sse41-stopwatch.o gmap_sse41-semaphore.o gmap_sse41-access.o gmap_sse41-filestring.o gmap_sse41-iit-read-univ.o gmap_sse41-iit-read.o gmap_sse41-md5.o gmap_sse41-bzip2.o gmap_sse41-fopen.o gmap_sse41-sequence.o gmap_sse41-reader.o gmap_sse41-genomicpos.o gmap_sse41-compress.o gmap_sse41-compress-write.o gmap_sse41-gbuffer.o gmap_sse41-genome.o gmap_sse41-popcount.o gmap_sse41-dinucl_bits.o gmap_sse41-genome_canonical.o gmap_sse41-genome-write.o gmap_sse41-bitpack64-read.o gmap_sse41-bitpack64-readtwo.o gmap_sse41-indexdb.o gmap_sse41-oligo.o gmap_sse41-block.o gmap_sse41-chrom.o gmap_sse41-segmentpos.o gmap_sse41-chrnum.o gmap_sse41-uinttable_rh.o gmap_sse41-gregion.o gmap_sse41-match.o gmap_sse41-matchpool.o gmap_sse41-diagnostic.o gmap_sse41-stage1.o gmap_sse41-diag.o gmap_sse41-diagpool.o gmap_sse41-cmet.o gmap_sse41-atoi.o gmap_sse41-orderstat.o gmap_sse41-oligoindex_hr.o gmap_sse41-intron.o gmap_sse41-maxent.o gmap_sse41-maxent_hr.o gmap_sse41-pair.o gmap_sse41-pairpool.o gmap_sse41-cellpool.o gmap_sse41-stage2.o gmap_sse41-doublelist.o gmap_sse41-smooth.o gmap_sse41-splicestringpool.o gmap_sse41-splicetrie_build.o gmap_sse41-splicetrie.o gmap_sse41-boyer-moore.o gmap_sse41-dynprog.o gmap_sse41-dynprog_simd.o gmap_sse41-dynprog_single.o gmap_sse41-dynprog_genome.o gmap_sse41-dynprog_cdna.o gmap_sse41-dynprog_end.o gmap_sse41-translation.o gmap_sse41-pbinom.o gmap_sse41-changepoint.o gmap_sse41-stage3.o gmap_sse41-request.o gmap_sse41-result.o gmap_sse41-output.o gmap_sse41-inbuffer.o gmap_sse41-samheader.o gmap_sse41-printbuffer.o gmap_sse41-outbuffer.o gmap_sse41-chimera.o gmap_sse41-datadir.o gmap_sse41-parserange.o gmap_sse41-getline.o gmap_sse41-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse41 gsnap_sse41-except.o gsnap_sse41-assert.o gsnap_sse41-mem.o gsnap_sse41-intlist.o gsnap_sse41-uintlist.o gsnap_sse41-list.o gsnap_sse41-littleendian.o gsnap_sse41-bigendian.o gsnap_sse41-univinterval.o gsnap_sse41-interval.o gsnap_sse41-stopwatch.o gsnap_sse41-semaphore.o gsnap_sse41-access.o gsnap_sse41-filestring.o gsnap_sse41-iit-read-univ.o gsnap_sse41-iit-read.o gsnap_sse41-bzip2.o gsnap_sse41-reader.o gsnap_sse41-genomicpos.o gsnap_sse41-compress.o gsnap_sse41-genome.o gsnap_sse41-transcriptome.o gsnap_sse41-popcount.o gsnap_sse41-genomebits.o gsnap_sse41-genomebits_consec.o gsnap_sse41-genomebits_count.o gsnap_sse41-genomebits_kmer.o gsnap_sse41-genomebits_indel.o gsnap_sse41-genomebits_decode.o gsnap_sse41-genomebits_mismatches.o gsnap_sse41-genomebits_trim.o gsnap_sse41-dinucl_bits.o gsnap_sse41-genome_sites.o gsnap_sse41-bitpack64-read.o gsnap_sse41-bitpack64-readtwo.o gsnap_sse41-mergeinfo.o gsnap_sse41-merge-diagonals-heap-uint4.o gsnap_sse41-merge-uint4.o gsnap_sse41-merge-diagonals-simd-uint4.o gsnap_sse41-indexdb.o gsnap_sse41-localdb-read.o gsnap_sse41-oligo.o gsnap_sse41-chrnum.o gsnap_sse41-maxent_hr.o gsnap_sse41-mapq.o gsnap_sse41-fopen.o gsnap_sse41-shortread.o gsnap_sse41-junction.o gsnap_sse41-concordance.o gsnap_sse41-simplepair.o gsnap_sse41-orderstat.o gsnap_sse41-intlistpool.o gsnap_sse41-uintlistpool.o gsnap_sse41-listpool.o gsnap_sse41-hitlistpool.o gsnap_sse41-pathpool.o gsnap_sse41-auxinfopool.o gsnap_sse41-pathstorepool.o gsnap_sse41-intron.o gsnap_sse41-gbuffer.o gsnap_sse41-select64-common.o gsnap_sse41-select64-ones.o gsnap_sse41-select64-zeroes.o gsnap_sse41-ef64.o gsnap_sse41-nr-x.o gsnap_sse41-knownsplicing.o gsnap_sse41-knownindels.o gsnap_sse41-splice.o gsnap_sse41-indel.o gsnap_sse41-spliceendsgen.o gsnap_sse41-spliceends.o gsnap_sse41-bitpack64-access.o gsnap_sse41-trdiag.o gsnap_sse41-trdiagpool.o gsnap_sse41-tr-extension-search.o gsnap_sse41-univdiag.o gsnap_sse41-univdiagpool.o gsnap_sse41-sedgesort.o gsnap_sse41-auxinfo.o gsnap_sse41-pathstore.o gsnap_sse41-altsplice.o gsnap_sse41-path.o gsnap_sse41-pathpair.o gsnap_sse41-path-solve.o gsnap_sse41-path-fusion.o gsnap_sse41-path-trim.o gsnap_sse41-path-eval.o gsnap_sse41-pathpair-eval.o gsnap_sse41-path-print-alignment.o gsnap_sse41-path-print-m8.o gsnap_sse41-path-print-sam.o gsnap_sse41-path-learn.o gsnap_sse41-method.o gsnap_sse41-doublelist.o gsnap_sse41-bitvector.o gsnap_sse41-transcriptpool.o gsnap_sse41-exon.o gsnap_sse41-transcript.o gsnap_sse41-trpathpool.o gsnap_sse41-trpath.o gsnap_sse41-trpath-solve.o gsnap_sse41-trpath-convert.o gsnap_sse41-trpath-eval.o gsnap_sse41-transcriptome-search.o gsnap_sse41-vectorpool.o gsnap_sse41-repair.o gsnap_sse41-transcript-remap.o gsnap_sse41-transcript-velocity.o gsnap_sse41-intersect-small.o gsnap_sse41-intersect-uint2.o gsnap_sse41-intersect-approx-uint4.o gsnap_sse41-intersect-approx-indices-uint4.o gsnap_sse41-intersect-wdups-indices.o gsnap_sse41-intersect-lower-small.o gsnap_sse41-intersect-higher-small.o gsnap_sse41-intersect-indices-small.o gsnap_sse41-intersect-indices2-small.o gsnap_sse41-intersect-concordance-uint4.o gsnap_sse41-kmer-search.o gsnap_sse41-extension-search.o gsnap_sse41-repetitive.o gsnap_sse41-uint8table.o gsnap_sse41-uinttable.o gsnap_sse41-stage1hr.o gsnap_sse41-stage1hr-single.o gsnap_sse41-stage1hr-paired.o gsnap_sse41-uinttableuint.o gsnap_sse41-tableuint.o gsnap_sse41-single-cell.o gsnap_sse41-request.o gsnap_sse41-resulthr.o gsnap_sse41-output.o gsnap_sse41-inbuffer.o gsnap_sse41-samheader.o gsnap_sse41-printbuffer.o gsnap_sse41-outbuffer.o gsnap_sse41-uintpairtable.o gsnap_sse41-splice-count.o gsnap_sse41-support.o gsnap_sse41-datadir.o gsnap_sse41-parserange.o gsnap_sse41-getline.o gsnap_sse41-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse41 gsnapl_sse41-except.o gsnapl_sse41-assert.o gsnapl_sse41-mem.o gsnapl_sse41-intlist.o gsnapl_sse41-uintlist.o gsnapl_sse41-uint8list.o gsnapl_sse41-list.o gsnapl_sse41-littleendian.o gsnapl_sse41-bigendian.o gsnapl_sse41-univinterval.o gsnapl_sse41-interval.o gsnapl_sse41-stopwatch.o gsnapl_sse41-semaphore.o gsnapl_sse41-access.o gsnapl_sse41-filestring.o gsnapl_sse41-iit-read-univ.o gsnapl_sse41-iit-read.o gsnapl_sse41-bzip2.o gsnapl_sse41-reader.o gsnapl_sse41-genomicpos.o gsnapl_sse41-compress.o gsnapl_sse41-genome.o gsnapl_sse41-transcriptome.o gsnapl_sse41-popcount.o gsnapl_sse41-genomebits.o gsnapl_sse41-genomebits_consec.o gsnapl_sse41-genomebits_count.o gsnapl_sse41-genomebits_kmer.o gsnapl_sse41-genomebits_indel.o gsnapl_sse41-genomebits_decode.o gsnapl_sse41-genomebits_mismatches.o gsnapl_sse41-genomebits_trim.o gsnapl_sse41-dinucl_bits.o gsnapl_sse41-genome_sites.o gsnapl_sse41-bitpack64-read.o gsnapl_sse41-bitpack64-readtwo.o gsnapl_sse41-mergeinfo.o gsnapl_sse41-merge-diagonals-heap-uint8.o gsnapl_sse41-merge-uint8.o gsnapl_sse41-merge-diagonals-simd-uint8.o gsnapl_sse41-merge-diagonals-heap-uint4.o gsnapl_sse41-merge-uint4.o gsnapl_sse41-merge-diagonals-simd-uint4.o gsnapl_sse41-indexdb.o gsnapl_sse41-localdb-read.o gsnapl_sse41-oligo.o gsnapl_sse41-chrnum.o gsnapl_sse41-maxent_hr.o gsnapl_sse41-mapq.o gsnapl_sse41-fopen.o gsnapl_sse41-shortread.o gsnapl_sse41-junction.o gsnapl_sse41-concordance.o gsnapl_sse41-simplepair.o gsnapl_sse41-orderstat.o gsnapl_sse41-intlistpool.o gsnapl_sse41-uintlistpool.o gsnapl_sse41-uint8listpool.o gsnapl_sse41-listpool.o gsnapl_sse41-hitlistpool.o gsnapl_sse41-pathpool.o gsnapl_sse41-auxinfopool.o gsnapl_sse41-pathstorepool.o gsnapl_sse41-intron.o gsnapl_sse41-gbuffer.o gsnapl_sse41-select64-common.o gsnapl_sse41-select64-ones.o gsnapl_sse41-select64-zeroes.o gsnapl_sse41-ef64.o gsnapl_sse41-nr-x.o gsnapl_sse41-knownsplicing.o gsnapl_sse41-knownindels.o gsnapl_sse41-splice.o gsnapl_sse41-indel.o gsnapl_sse41-spliceendsgen.o gsnapl_sse41-spliceends.o gsnapl_sse41-bitpack64-access.o gsnapl_sse41-trdiag.o gsnapl_sse41-trdiagpool.o gsnapl_sse41-tr-extension-search.o gsnapl_sse41-univdiag.o gsnapl_sse41-univdiagpool.o gsnapl_sse41-sedgesort.o gsnapl_sse41-auxinfo.o gsnapl_sse41-pathstore.o gsnapl_sse41-altsplice.o gsnapl_sse41-path.o gsnapl_sse41-pathpair.o gsnapl_sse41-path-solve.o gsnapl_sse41-path-fusion.o gsnapl_sse41-path-trim.o gsnapl_sse41-path-eval.o gsnapl_sse41-pathpair-eval.o gsnapl_sse41-path-print-alignment.o gsnapl_sse41-path-print-m8.o gsnapl_sse41-path-print-sam.o gsnapl_sse41-path-learn.o gsnapl_sse41-method.o gsnapl_sse41-doublelist.o gsnapl_sse41-bitvector.o gsnapl_sse41-transcriptpool.o gsnapl_sse41-exon.o gsnapl_sse41-transcript.o gsnapl_sse41-trpathpool.o gsnapl_sse41-trpath.o gsnapl_sse41-trpath-solve.o gsnapl_sse41-trpath-convert.o gsnapl_sse41-trpath-eval.o gsnapl_sse41-transcriptome-search.o gsnapl_sse41-vectorpool.o gsnapl_sse41-repair.o gsnapl_sse41-transcript-remap.o gsnapl_sse41-transcript-velocity.o gsnapl_sse41-intersect-large.o gsnapl_sse41-intersect-small.o gsnapl_sse41-intersect-uint2.o gsnapl_sse41-intersect-approx-uint4.o gsnapl_sse41-intersect-approx-uint8.o gsnapl_sse41-intersect-approx-indices-uint8.o gsnapl_sse41-intersect-wdups-indices.o gsnapl_sse41-intersect-lower-large.o gsnapl_sse41-intersect-higher-large.o gsnapl_sse41-intersect-indices-small.o gsnapl_sse41-intersect-indices2-large.o gsnapl_sse41-intersect-indices-uint8.o gsnapl_sse41-intersect-concordance-uint8.o gsnapl_sse41-kmer-search.o gsnapl_sse41-extension-search.o gsnapl_sse41-repetitive.o gsnapl_sse41-uint8table.o gsnapl_sse41-stage1hr.o gsnapl_sse41-stage1hr-single.o gsnapl_sse41-stage1hr-paired.o gsnapl_sse41-uint8tableuint.o gsnapl_sse41-tableuint.o gsnapl_sse41-single-cell.o gsnapl_sse41-request.o gsnapl_sse41-resulthr.o gsnapl_sse41-output.o gsnapl_sse41-inbuffer.o gsnapl_sse41-samheader.o gsnapl_sse41-printbuffer.o gsnapl_sse41-outbuffer.o gsnapl_sse41-uint8pairtable.o gsnapl_sse41-splice-count.o gsnapl_sse41-support.o gsnapl_sse41-datadir.o gsnapl_sse41-parserange.o gsnapl_sse41-getline.o gsnapl_sse41-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites chmod +x fa_coords chmod +x psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gtf_genes chmod +x psl_introns chmod +x psl_genes chmod +x ensembl_genes chmod +x gtf_splicesites chmod +x gtf_introns chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites chmod +x gff3_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x gff3_genes chmod +x dbsnp_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' dh_auto_build --builddir build_sse42 cd build_sse42 && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c ../../src/indexdb.c: In function 'positions_read_multiple_large': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse42 gmap_sse42-except.o gmap_sse42-assert.o gmap_sse42-mem.o gmap_sse42-intlist.o gmap_sse42-uintlist.o gmap_sse42-list.o gmap_sse42-littleendian.o gmap_sse42-bigendian.o gmap_sse42-univinterval.o gmap_sse42-interval.o gmap_sse42-stopwatch.o gmap_sse42-semaphore.o gmap_sse42-access.o gmap_sse42-filestring.o gmap_sse42-iit-read-univ.o gmap_sse42-iit-read.o gmap_sse42-md5.o gmap_sse42-bzip2.o gmap_sse42-fopen.o gmap_sse42-sequence.o gmap_sse42-reader.o gmap_sse42-genomicpos.o gmap_sse42-compress.o gmap_sse42-compress-write.o gmap_sse42-gbuffer.o gmap_sse42-genome.o gmap_sse42-popcount.o gmap_sse42-dinucl_bits.o gmap_sse42-genome_canonical.o gmap_sse42-genome-write.o gmap_sse42-bitpack64-read.o gmap_sse42-bitpack64-readtwo.o gmap_sse42-indexdb.o gmap_sse42-oligo.o gmap_sse42-block.o gmap_sse42-chrom.o gmap_sse42-segmentpos.o gmap_sse42-chrnum.o gmap_sse42-uinttable_rh.o gmap_sse42-gregion.o gmap_sse42-match.o gmap_sse42-matchpool.o gmap_sse42-diagnostic.o gmap_sse42-stage1.o gmap_sse42-diag.o gmap_sse42-diagpool.o gmap_sse42-cmet.o gmap_sse42-atoi.o gmap_sse42-orderstat.o gmap_sse42-oligoindex_hr.o gmap_sse42-intron.o gmap_sse42-maxent.o gmap_sse42-maxent_hr.o gmap_sse42-pair.o gmap_sse42-pairpool.o gmap_sse42-cellpool.o gmap_sse42-stage2.o gmap_sse42-doublelist.o gmap_sse42-smooth.o gmap_sse42-splicestringpool.o gmap_sse42-splicetrie_build.o gmap_sse42-splicetrie.o gmap_sse42-boyer-moore.o gmap_sse42-dynprog.o gmap_sse42-dynprog_simd.o gmap_sse42-dynprog_single.o gmap_sse42-dynprog_genome.o gmap_sse42-dynprog_cdna.o gmap_sse42-dynprog_end.o gmap_sse42-translation.o gmap_sse42-pbinom.o gmap_sse42-changepoint.o gmap_sse42-stage3.o gmap_sse42-request.o gmap_sse42-result.o gmap_sse42-output.o gmap_sse42-inbuffer.o gmap_sse42-samheader.o gmap_sse42-printbuffer.o gmap_sse42-outbuffer.o gmap_sse42-chimera.o gmap_sse42-datadir.o gmap_sse42-parserange.o gmap_sse42-getline.o gmap_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse42 gmapl_sse42-except.o gmapl_sse42-assert.o gmapl_sse42-mem.o gmapl_sse42-intlist.o gmapl_sse42-uintlist.o gmapl_sse42-uint8list.o gmapl_sse42-list.o gmapl_sse42-littleendian.o gmapl_sse42-bigendian.o gmapl_sse42-univinterval.o gmapl_sse42-interval.o gmapl_sse42-stopwatch.o gmapl_sse42-semaphore.o gmapl_sse42-access.o gmapl_sse42-filestring.o gmapl_sse42-iit-read-univ.o gmapl_sse42-iit-read.o gmapl_sse42-md5.o gmapl_sse42-bzip2.o gmapl_sse42-fopen.o gmapl_sse42-sequence.o gmapl_sse42-reader.o gmapl_sse42-genomicpos.o gmapl_sse42-compress.o gmapl_sse42-compress-write.o gmapl_sse42-gbuffer.o gmapl_sse42-genome.o gmapl_sse42-popcount.o gmapl_sse42-dinucl_bits.o gmapl_sse42-genome_canonical.o gmapl_sse42-genome-write.o gmapl_sse42-bitpack64-read.o gmapl_sse42-bitpack64-readtwo.o gmapl_sse42-indexdb.o gmapl_sse42-oligo.o gmapl_sse42-block.o gmapl_sse42-chrom.o gmapl_sse42-segmentpos.o gmapl_sse42-chrnum.o gmapl_sse42-uinttable_rh.o gmapl_sse42-uint8table_rh.o gmapl_sse42-gregion.o gmapl_sse42-match.o gmapl_sse42-matchpool.o gmapl_sse42-diagnostic.o gmapl_sse42-stage1.o gmapl_sse42-diag.o gmapl_sse42-diagpool.o gmapl_sse42-cmet.o gmapl_sse42-atoi.o gmapl_sse42-orderstat.o gmapl_sse42-oligoindex_hr.o gmapl_sse42-intron.o gmapl_sse42-maxent.o gmapl_sse42-maxent_hr.o gmapl_sse42-pair.o gmapl_sse42-pairpool.o gmapl_sse42-cellpool.o gmapl_sse42-stage2.o gmapl_sse42-doublelist.o gmapl_sse42-smooth.o gmapl_sse42-splicestringpool.o gmapl_sse42-splicetrie_build.o gmapl_sse42-splicetrie.o gmapl_sse42-boyer-moore.o gmapl_sse42-dynprog.o gmapl_sse42-dynprog_simd.o gmapl_sse42-dynprog_single.o gmapl_sse42-dynprog_genome.o gmapl_sse42-dynprog_cdna.o gmapl_sse42-dynprog_end.o gmapl_sse42-translation.o gmapl_sse42-pbinom.o gmapl_sse42-changepoint.o gmapl_sse42-stage3.o gmapl_sse42-request.o gmapl_sse42-result.o gmapl_sse42-output.o gmapl_sse42-inbuffer.o gmapl_sse42-samheader.o gmapl_sse42-printbuffer.o gmapl_sse42-outbuffer.o gmapl_sse42-chimera.o gmapl_sse42-datadir.o gmapl_sse42-parserange.o gmapl_sse42-getline.o gmapl_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse42 gsnap_sse42-except.o gsnap_sse42-assert.o gsnap_sse42-mem.o gsnap_sse42-intlist.o gsnap_sse42-uintlist.o gsnap_sse42-list.o gsnap_sse42-littleendian.o gsnap_sse42-bigendian.o gsnap_sse42-univinterval.o gsnap_sse42-interval.o gsnap_sse42-stopwatch.o gsnap_sse42-semaphore.o gsnap_sse42-access.o gsnap_sse42-filestring.o gsnap_sse42-iit-read-univ.o gsnap_sse42-iit-read.o gsnap_sse42-bzip2.o gsnap_sse42-reader.o gsnap_sse42-genomicpos.o gsnap_sse42-compress.o gsnap_sse42-genome.o gsnap_sse42-transcriptome.o gsnap_sse42-popcount.o gsnap_sse42-genomebits.o gsnap_sse42-genomebits_consec.o gsnap_sse42-genomebits_count.o gsnap_sse42-genomebits_kmer.o gsnap_sse42-genomebits_indel.o gsnap_sse42-genomebits_decode.o gsnap_sse42-genomebits_mismatches.o gsnap_sse42-genomebits_trim.o gsnap_sse42-dinucl_bits.o gsnap_sse42-genome_sites.o gsnap_sse42-bitpack64-read.o gsnap_sse42-bitpack64-readtwo.o gsnap_sse42-mergeinfo.o gsnap_sse42-merge-diagonals-heap-uint4.o gsnap_sse42-merge-uint4.o gsnap_sse42-merge-diagonals-simd-uint4.o gsnap_sse42-indexdb.o gsnap_sse42-localdb-read.o gsnap_sse42-oligo.o gsnap_sse42-chrnum.o gsnap_sse42-maxent_hr.o gsnap_sse42-mapq.o gsnap_sse42-fopen.o gsnap_sse42-shortread.o gsnap_sse42-junction.o gsnap_sse42-concordance.o gsnap_sse42-simplepair.o gsnap_sse42-orderstat.o gsnap_sse42-intlistpool.o gsnap_sse42-uintlistpool.o gsnap_sse42-listpool.o gsnap_sse42-hitlistpool.o gsnap_sse42-pathpool.o gsnap_sse42-auxinfopool.o gsnap_sse42-pathstorepool.o gsnap_sse42-intron.o gsnap_sse42-gbuffer.o gsnap_sse42-select64-common.o gsnap_sse42-select64-ones.o gsnap_sse42-select64-zeroes.o gsnap_sse42-ef64.o gsnap_sse42-nr-x.o gsnap_sse42-knownsplicing.o gsnap_sse42-knownindels.o gsnap_sse42-splice.o gsnap_sse42-indel.o gsnap_sse42-spliceendsgen.o gsnap_sse42-spliceends.o gsnap_sse42-bitpack64-access.o gsnap_sse42-trdiag.o gsnap_sse42-trdiagpool.o gsnap_sse42-tr-extension-search.o gsnap_sse42-univdiag.o gsnap_sse42-univdiagpool.o gsnap_sse42-sedgesort.o gsnap_sse42-auxinfo.o gsnap_sse42-pathstore.o gsnap_sse42-altsplice.o gsnap_sse42-path.o gsnap_sse42-pathpair.o gsnap_sse42-path-solve.o gsnap_sse42-path-fusion.o gsnap_sse42-path-trim.o gsnap_sse42-path-eval.o gsnap_sse42-pathpair-eval.o gsnap_sse42-path-print-alignment.o gsnap_sse42-path-print-m8.o gsnap_sse42-path-print-sam.o gsnap_sse42-path-learn.o gsnap_sse42-method.o gsnap_sse42-doublelist.o gsnap_sse42-bitvector.o gsnap_sse42-transcriptpool.o gsnap_sse42-exon.o gsnap_sse42-transcript.o gsnap_sse42-trpathpool.o gsnap_sse42-trpath.o gsnap_sse42-trpath-solve.o gsnap_sse42-trpath-convert.o gsnap_sse42-trpath-eval.o gsnap_sse42-transcriptome-search.o gsnap_sse42-vectorpool.o gsnap_sse42-repair.o gsnap_sse42-transcript-remap.o gsnap_sse42-transcript-velocity.o gsnap_sse42-intersect-small.o gsnap_sse42-intersect-uint2.o gsnap_sse42-intersect-approx-uint4.o gsnap_sse42-intersect-approx-indices-uint4.o gsnap_sse42-intersect-wdups-indices.o gsnap_sse42-intersect-lower-small.o gsnap_sse42-intersect-higher-small.o gsnap_sse42-intersect-indices-small.o gsnap_sse42-intersect-indices2-small.o gsnap_sse42-intersect-concordance-uint4.o gsnap_sse42-kmer-search.o gsnap_sse42-extension-search.o gsnap_sse42-repetitive.o gsnap_sse42-uint8table.o gsnap_sse42-uinttable.o gsnap_sse42-stage1hr.o gsnap_sse42-stage1hr-single.o gsnap_sse42-stage1hr-paired.o gsnap_sse42-uinttableuint.o gsnap_sse42-tableuint.o gsnap_sse42-single-cell.o gsnap_sse42-request.o gsnap_sse42-resulthr.o gsnap_sse42-output.o gsnap_sse42-inbuffer.o gsnap_sse42-samheader.o gsnap_sse42-printbuffer.o gsnap_sse42-outbuffer.o gsnap_sse42-uintpairtable.o gsnap_sse42-splice-count.o gsnap_sse42-support.o gsnap_sse42-datadir.o gsnap_sse42-parserange.o gsnap_sse42-getline.o gsnap_sse42-gsnap.o -lz -lbz2 -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse42 gsnapl_sse42-except.o gsnapl_sse42-assert.o gsnapl_sse42-mem.o gsnapl_sse42-intlist.o gsnapl_sse42-uintlist.o gsnapl_sse42-uint8list.o gsnapl_sse42-list.o gsnapl_sse42-littleendian.o gsnapl_sse42-bigendian.o gsnapl_sse42-univinterval.o gsnapl_sse42-interval.o gsnapl_sse42-stopwatch.o gsnapl_sse42-semaphore.o gsnapl_sse42-access.o gsnapl_sse42-filestring.o gsnapl_sse42-iit-read-univ.o gsnapl_sse42-iit-read.o gsnapl_sse42-bzip2.o gsnapl_sse42-reader.o gsnapl_sse42-genomicpos.o gsnapl_sse42-compress.o gsnapl_sse42-genome.o gsnapl_sse42-transcriptome.o gsnapl_sse42-popcount.o gsnapl_sse42-genomebits.o gsnapl_sse42-genomebits_consec.o gsnapl_sse42-genomebits_count.o gsnapl_sse42-genomebits_kmer.o gsnapl_sse42-genomebits_indel.o gsnapl_sse42-genomebits_decode.o gsnapl_sse42-genomebits_mismatches.o gsnapl_sse42-genomebits_trim.o gsnapl_sse42-dinucl_bits.o gsnapl_sse42-genome_sites.o gsnapl_sse42-bitpack64-read.o gsnapl_sse42-bitpack64-readtwo.o gsnapl_sse42-mergeinfo.o gsnapl_sse42-merge-diagonals-heap-uint8.o gsnapl_sse42-merge-uint8.o gsnapl_sse42-merge-diagonals-simd-uint8.o gsnapl_sse42-merge-diagonals-heap-uint4.o gsnapl_sse42-merge-uint4.o gsnapl_sse42-merge-diagonals-simd-uint4.o gsnapl_sse42-indexdb.o gsnapl_sse42-localdb-read.o gsnapl_sse42-oligo.o gsnapl_sse42-chrnum.o gsnapl_sse42-maxent_hr.o gsnapl_sse42-mapq.o gsnapl_sse42-fopen.o gsnapl_sse42-shortread.o gsnapl_sse42-junction.o gsnapl_sse42-concordance.o gsnapl_sse42-simplepair.o gsnapl_sse42-orderstat.o gsnapl_sse42-intlistpool.o gsnapl_sse42-uintlistpool.o gsnapl_sse42-uint8listpool.o gsnapl_sse42-listpool.o gsnapl_sse42-hitlistpool.o gsnapl_sse42-pathpool.o gsnapl_sse42-auxinfopool.o gsnapl_sse42-pathstorepool.o gsnapl_sse42-intron.o gsnapl_sse42-gbuffer.o gsnapl_sse42-select64-common.o gsnapl_sse42-select64-ones.o gsnapl_sse42-select64-zeroes.o gsnapl_sse42-ef64.o gsnapl_sse42-nr-x.o gsnapl_sse42-knownsplicing.o gsnapl_sse42-knownindels.o gsnapl_sse42-splice.o gsnapl_sse42-indel.o gsnapl_sse42-spliceendsgen.o gsnapl_sse42-spliceends.o gsnapl_sse42-bitpack64-access.o gsnapl_sse42-trdiag.o gsnapl_sse42-trdiagpool.o gsnapl_sse42-tr-extension-search.o gsnapl_sse42-univdiag.o gsnapl_sse42-univdiagpool.o gsnapl_sse42-sedgesort.o gsnapl_sse42-auxinfo.o gsnapl_sse42-pathstore.o gsnapl_sse42-altsplice.o gsnapl_sse42-path.o gsnapl_sse42-pathpair.o gsnapl_sse42-path-solve.o gsnapl_sse42-path-fusion.o gsnapl_sse42-path-trim.o gsnapl_sse42-path-eval.o gsnapl_sse42-pathpair-eval.o gsnapl_sse42-path-print-alignment.o gsnapl_sse42-path-print-m8.o gsnapl_sse42-path-print-sam.o gsnapl_sse42-path-learn.o gsnapl_sse42-method.o gsnapl_sse42-doublelist.o gsnapl_sse42-bitvector.o gsnapl_sse42-transcriptpool.o gsnapl_sse42-exon.o gsnapl_sse42-transcript.o gsnapl_sse42-trpathpool.o gsnapl_sse42-trpath.o gsnapl_sse42-trpath-solve.o gsnapl_sse42-trpath-convert.o gsnapl_sse42-trpath-eval.o gsnapl_sse42-transcriptome-search.o gsnapl_sse42-vectorpool.o gsnapl_sse42-repair.o gsnapl_sse42-transcript-remap.o gsnapl_sse42-transcript-velocity.o gsnapl_sse42-intersect-large.o gsnapl_sse42-intersect-small.o gsnapl_sse42-intersect-uint2.o gsnapl_sse42-intersect-approx-uint4.o gsnapl_sse42-intersect-approx-uint8.o gsnapl_sse42-intersect-approx-indices-uint8.o gsnapl_sse42-intersect-wdups-indices.o gsnapl_sse42-intersect-lower-large.o gsnapl_sse42-intersect-higher-large.o gsnapl_sse42-intersect-indices-small.o gsnapl_sse42-intersect-indices2-large.o gsnapl_sse42-intersect-indices-uint8.o gsnapl_sse42-intersect-concordance-uint8.o gsnapl_sse42-kmer-search.o gsnapl_sse42-extension-search.o gsnapl_sse42-repetitive.o gsnapl_sse42-uint8table.o gsnapl_sse42-stage1hr.o gsnapl_sse42-stage1hr-single.o gsnapl_sse42-stage1hr-paired.o gsnapl_sse42-uint8tableuint.o gsnapl_sse42-tableuint.o gsnapl_sse42-single-cell.o gsnapl_sse42-request.o gsnapl_sse42-resulthr.o gsnapl_sse42-output.o gsnapl_sse42-inbuffer.o gsnapl_sse42-samheader.o gsnapl_sse42-printbuffer.o gsnapl_sse42-outbuffer.o gsnapl_sse42-uint8pairtable.o gsnapl_sse42-splice-count.o gsnapl_sse42-support.o gsnapl_sse42-datadir.o gsnapl_sse42-parserange.o gsnapl_sse42-getline.o gsnapl_sse42-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites chmod +x gmap_process cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x gmap_build chmod +x gmap_cat chmod +x md_coords chmod +x fa_coords chmod +x psl_splicesites cp ensembl_genes.pl ensembl_genes chmod +x psl_introns chmod +x psl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x ensembl_genes cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gtf_splicesites cp gff3_genes.pl gff3_genes chmod +x gtf_introns chmod +x gtf_genes chmod +x gtf_transcript_splicesites cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_splicesites chmod +x gff3_introns chmod +x gff3_genes cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x dbsnp_iit chmod +x vcf_iit chmod +x gvf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' dh_auto_build --builddir build_avx2 cd build_avx2 && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-dinucl_bits.o gmap_avx2-genome_canonical.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-printbuffer.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-dinucl_bits.o gmapl_avx2-genome_canonical.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-uint8table_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-printbuffer.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genomebits.o gsnap_avx2-genomebits_consec.o gsnap_avx2-genomebits_count.o gsnap_avx2-genomebits_kmer.o gsnap_avx2-genomebits_indel.o gsnap_avx2-genomebits_decode.o gsnap_avx2-genomebits_mismatches.o gsnap_avx2-genomebits_trim.o gsnap_avx2-dinucl_bits.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-mergeinfo.o gsnap_avx2-merge-diagonals-heap-uint4.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-localdb-read.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-junction.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-pathpool.o gsnap_avx2-auxinfopool.o gsnap_avx2-pathstorepool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-select64-common.o gsnap_avx2-select64-ones.o gsnap_avx2-select64-zeroes.o gsnap_avx2-ef64.o gsnap_avx2-nr-x.o gsnap_avx2-knownsplicing.o gsnap_avx2-knownindels.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-spliceendsgen.o gsnap_avx2-spliceends.o gsnap_avx2-bitpack64-access.o gsnap_avx2-trdiag.o gsnap_avx2-trdiagpool.o gsnap_avx2-tr-extension-search.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-auxinfo.o gsnap_avx2-pathstore.o gsnap_avx2-altsplice.o gsnap_avx2-path.o gsnap_avx2-pathpair.o gsnap_avx2-path-solve.o gsnap_avx2-path-fusion.o gsnap_avx2-path-trim.o gsnap_avx2-path-eval.o gsnap_avx2-pathpair-eval.o gsnap_avx2-path-print-alignment.o gsnap_avx2-path-print-m8.o gsnap_avx2-path-print-sam.o gsnap_avx2-path-learn.o gsnap_avx2-method.o gsnap_avx2-doublelist.o gsnap_avx2-bitvector.o gsnap_avx2-transcriptpool.o gsnap_avx2-exon.o gsnap_avx2-transcript.o gsnap_avx2-trpathpool.o gsnap_avx2-trpath.o gsnap_avx2-trpath-solve.o gsnap_avx2-trpath-convert.o gsnap_avx2-trpath-eval.o gsnap_avx2-transcriptome-search.o gsnap_avx2-vectorpool.o gsnap_avx2-repair.o gsnap_avx2-transcript-remap.o gsnap_avx2-transcript-velocity.o gsnap_avx2-intersect-small.o gsnap_avx2-intersect-uint2.o gsnap_avx2-intersect-approx-uint4.o gsnap_avx2-intersect-approx-indices-uint4.o gsnap_avx2-intersect-wdups-indices.o gsnap_avx2-intersect-lower-small.o gsnap_avx2-intersect-higher-small.o gsnap_avx2-intersect-indices-small.o gsnap_avx2-intersect-indices2-small.o gsnap_avx2-intersect-concordance-uint4.o gsnap_avx2-kmer-search.o gsnap_avx2-extension-search.o gsnap_avx2-repetitive.o gsnap_avx2-uint8table.o gsnap_avx2-uinttable.o gsnap_avx2-stage1hr.o gsnap_avx2-stage1hr-single.o gsnap_avx2-stage1hr-paired.o gsnap_avx2-uinttableuint.o gsnap_avx2-tableuint.o gsnap_avx2-single-cell.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-printbuffer.o gsnap_avx2-outbuffer.o gsnap_avx2-uintpairtable.o gsnap_avx2-splice-count.o gsnap_avx2-support.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-gsnap.o -lz -lbz2 -lm ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx2 gsnapl_avx2-except.o gsnapl_avx2-assert.o gsnapl_avx2-mem.o gsnapl_avx2-intlist.o gsnapl_avx2-uintlist.o gsnapl_avx2-uint8list.o gsnapl_avx2-list.o gsnapl_avx2-littleendian.o gsnapl_avx2-bigendian.o gsnapl_avx2-univinterval.o gsnapl_avx2-interval.o gsnapl_avx2-stopwatch.o gsnapl_avx2-semaphore.o gsnapl_avx2-access.o gsnapl_avx2-filestring.o gsnapl_avx2-iit-read-univ.o gsnapl_avx2-iit-read.o gsnapl_avx2-bzip2.o gsnapl_avx2-reader.o gsnapl_avx2-genomicpos.o gsnapl_avx2-compress.o gsnapl_avx2-genome.o gsnapl_avx2-transcriptome.o gsnapl_avx2-popcount.o gsnapl_avx2-genomebits.o gsnapl_avx2-genomebits_consec.o gsnapl_avx2-genomebits_count.o gsnapl_avx2-genomebits_kmer.o gsnapl_avx2-genomebits_indel.o gsnapl_avx2-genomebits_decode.o gsnapl_avx2-genomebits_mismatches.o gsnapl_avx2-genomebits_trim.o gsnapl_avx2-dinucl_bits.o gsnapl_avx2-genome_sites.o gsnapl_avx2-bitpack64-read.o gsnapl_avx2-bitpack64-readtwo.o gsnapl_avx2-mergeinfo.o gsnapl_avx2-merge-diagonals-heap-uint8.o gsnapl_avx2-merge-uint8.o gsnapl_avx2-merge-diagonals-simd-uint8.o gsnapl_avx2-merge-diagonals-heap-uint4.o gsnapl_avx2-merge-uint4.o gsnapl_avx2-merge-diagonals-simd-uint4.o gsnapl_avx2-indexdb.o gsnapl_avx2-localdb-read.o gsnapl_avx2-oligo.o gsnapl_avx2-chrnum.o gsnapl_avx2-maxent_hr.o gsnapl_avx2-mapq.o gsnapl_avx2-fopen.o gsnapl_avx2-shortread.o gsnapl_avx2-junction.o gsnapl_avx2-concordance.o gsnapl_avx2-simplepair.o gsnapl_avx2-orderstat.o gsnapl_avx2-intlistpool.o gsnapl_avx2-uintlistpool.o gsnapl_avx2-uint8listpool.o gsnapl_avx2-listpool.o gsnapl_avx2-hitlistpool.o gsnapl_avx2-pathpool.o gsnapl_avx2-auxinfopool.o gsnapl_avx2-pathstorepool.o gsnapl_avx2-intron.o gsnapl_avx2-gbuffer.o gsnapl_avx2-select64-common.o gsnapl_avx2-select64-ones.o gsnapl_avx2-select64-zeroes.o gsnapl_avx2-ef64.o gsnapl_avx2-nr-x.o gsnapl_avx2-knownsplicing.o gsnapl_avx2-knownindels.o gsnapl_avx2-splice.o gsnapl_avx2-indel.o gsnapl_avx2-spliceendsgen.o gsnapl_avx2-spliceends.o gsnapl_avx2-bitpack64-access.o gsnapl_avx2-trdiag.o gsnapl_avx2-trdiagpool.o gsnapl_avx2-tr-extension-search.o gsnapl_avx2-univdiag.o gsnapl_avx2-univdiagpool.o gsnapl_avx2-sedgesort.o gsnapl_avx2-auxinfo.o gsnapl_avx2-pathstore.o gsnapl_avx2-altsplice.o gsnapl_avx2-path.o gsnapl_avx2-pathpair.o gsnapl_avx2-path-solve.o gsnapl_avx2-path-fusion.o gsnapl_avx2-path-trim.o gsnapl_avx2-path-eval.o gsnapl_avx2-pathpair-eval.o gsnapl_avx2-path-print-alignment.o gsnapl_avx2-path-print-m8.o gsnapl_avx2-path-print-sam.o gsnapl_avx2-path-learn.o gsnapl_avx2-method.o gsnapl_avx2-doublelist.o gsnapl_avx2-bitvector.o gsnapl_avx2-transcriptpool.o gsnapl_avx2-exon.o gsnapl_avx2-transcript.o gsnapl_avx2-trpathpool.o gsnapl_avx2-trpath.o gsnapl_avx2-trpath-solve.o gsnapl_avx2-trpath-convert.o gsnapl_avx2-trpath-eval.o gsnapl_avx2-transcriptome-search.o gsnapl_avx2-vectorpool.o gsnapl_avx2-repair.o gsnapl_avx2-transcript-remap.o gsnapl_avx2-transcript-velocity.o gsnapl_avx2-intersect-large.o gsnapl_avx2-intersect-small.o gsnapl_avx2-intersect-uint2.o gsnapl_avx2-intersect-approx-uint4.o gsnapl_avx2-intersect-approx-uint8.o gsnapl_avx2-intersect-approx-indices-uint8.o gsnapl_avx2-intersect-wdups-indices.o gsnapl_avx2-intersect-lower-large.o gsnapl_avx2-intersect-higher-large.o gsnapl_avx2-intersect-indices-small.o gsnapl_avx2-intersect-indices2-large.o gsnapl_avx2-intersect-indices-uint8.o gsnapl_avx2-intersect-concordance-uint8.o gsnapl_avx2-kmer-search.o gsnapl_avx2-extension-search.o gsnapl_avx2-repetitive.o gsnapl_avx2-uint8table.o gsnapl_avx2-stage1hr.o gsnapl_avx2-stage1hr-single.o gsnapl_avx2-stage1hr-paired.o gsnapl_avx2-uint8tableuint.o gsnapl_avx2-tableuint.o gsnapl_avx2-single-cell.o gsnapl_avx2-request.o gsnapl_avx2-resulthr.o gsnapl_avx2-output.o gsnapl_avx2-inbuffer.o gsnapl_avx2-samheader.o gsnapl_avx2-printbuffer.o gsnapl_avx2-outbuffer.o gsnapl_avx2-uint8pairtable.o gsnapl_avx2-splice-count.o gsnapl_avx2-support.o gsnapl_avx2-datadir.o gsnapl_avx2-parserange.o gsnapl_avx2-getline.o gsnapl_avx2-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x fa_coords cp ensembl_genes.pl ensembl_genes chmod +x psl_splicesites chmod +x psl_introns chmod +x psl_genes chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_introns chmod +x gtf_transcript_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites chmod +x gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x dbsnp_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' dh_auto_build --builddir build_avx512 cd build_avx512 && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx512 gmap_avx512-except.o gmap_avx512-assert.o gmap_avx512-mem.o gmap_avx512-intlist.o gmap_avx512-uintlist.o gmap_avx512-list.o gmap_avx512-littleendian.o gmap_avx512-bigendian.o gmap_avx512-univinterval.o gmap_avx512-interval.o gmap_avx512-stopwatch.o gmap_avx512-semaphore.o gmap_avx512-access.o gmap_avx512-filestring.o gmap_avx512-iit-read-univ.o gmap_avx512-iit-read.o gmap_avx512-md5.o gmap_avx512-bzip2.o gmap_avx512-fopen.o gmap_avx512-sequence.o gmap_avx512-reader.o gmap_avx512-genomicpos.o gmap_avx512-compress.o gmap_avx512-compress-write.o gmap_avx512-gbuffer.o gmap_avx512-genome.o gmap_avx512-popcount.o gmap_avx512-dinucl_bits.o gmap_avx512-genome_canonical.o gmap_avx512-genome-write.o gmap_avx512-bitpack64-read.o gmap_avx512-bitpack64-readtwo.o gmap_avx512-indexdb.o gmap_avx512-oligo.o gmap_avx512-block.o gmap_avx512-chrom.o gmap_avx512-segmentpos.o gmap_avx512-chrnum.o gmap_avx512-uinttable_rh.o gmap_avx512-gregion.o gmap_avx512-match.o gmap_avx512-matchpool.o gmap_avx512-diagnostic.o gmap_avx512-stage1.o gmap_avx512-diag.o gmap_avx512-diagpool.o gmap_avx512-cmet.o gmap_avx512-atoi.o gmap_avx512-orderstat.o gmap_avx512-oligoindex_hr.o gmap_avx512-intron.o gmap_avx512-maxent.o gmap_avx512-maxent_hr.o gmap_avx512-pair.o gmap_avx512-pairpool.o gmap_avx512-cellpool.o gmap_avx512-stage2.o gmap_avx512-doublelist.o gmap_avx512-smooth.o gmap_avx512-splicestringpool.o gmap_avx512-splicetrie_build.o gmap_avx512-splicetrie.o gmap_avx512-boyer-moore.o gmap_avx512-dynprog.o gmap_avx512-dynprog_simd.o gmap_avx512-dynprog_single.o gmap_avx512-dynprog_genome.o gmap_avx512-dynprog_cdna.o gmap_avx512-dynprog_end.o gmap_avx512-translation.o gmap_avx512-pbinom.o gmap_avx512-changepoint.o gmap_avx512-stage3.o gmap_avx512-request.o gmap_avx512-result.o gmap_avx512-output.o gmap_avx512-inbuffer.o gmap_avx512-samheader.o gmap_avx512-printbuffer.o gmap_avx512-outbuffer.o gmap_avx512-chimera.o gmap_avx512-datadir.o gmap_avx512-parserange.o gmap_avx512-getline.o gmap_avx512-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx512 gsnap_avx512-except.o gsnap_avx512-assert.o gsnap_avx512-mem.o gsnap_avx512-intlist.o gsnap_avx512-uintlist.o gsnap_avx512-list.o gsnap_avx512-littleendian.o gsnap_avx512-bigendian.o gsnap_avx512-univinterval.o gsnap_avx512-interval.o gsnap_avx512-stopwatch.o gsnap_avx512-semaphore.o gsnap_avx512-access.o gsnap_avx512-filestring.o gsnap_avx512-iit-read-univ.o gsnap_avx512-iit-read.o gsnap_avx512-bzip2.o gsnap_avx512-reader.o gsnap_avx512-genomicpos.o gsnap_avx512-compress.o gsnap_avx512-genome.o gsnap_avx512-transcriptome.o gsnap_avx512-popcount.o gsnap_avx512-genomebits.o gsnap_avx512-genomebits_consec.o gsnap_avx512-genomebits_count.o gsnap_avx512-genomebits_kmer.o gsnap_avx512-genomebits_indel.o gsnap_avx512-genomebits_decode.o gsnap_avx512-genomebits_mismatches.o gsnap_avx512-genomebits_trim.o gsnap_avx512-dinucl_bits.o gsnap_avx512-genome_sites.o gsnap_avx512-bitpack64-read.o gsnap_avx512-bitpack64-readtwo.o gsnap_avx512-mergeinfo.o gsnap_avx512-merge-diagonals-heap-uint4.o gsnap_avx512-merge-uint4.o gsnap_avx512-merge-diagonals-simd-uint4.o gsnap_avx512-indexdb.o gsnap_avx512-localdb-read.o gsnap_avx512-oligo.o gsnap_avx512-chrnum.o gsnap_avx512-maxent_hr.o gsnap_avx512-mapq.o gsnap_avx512-fopen.o gsnap_avx512-shortread.o gsnap_avx512-junction.o gsnap_avx512-concordance.o gsnap_avx512-simplepair.o gsnap_avx512-orderstat.o gsnap_avx512-intlistpool.o gsnap_avx512-uintlistpool.o gsnap_avx512-listpool.o gsnap_avx512-hitlistpool.o gsnap_avx512-pathpool.o gsnap_avx512-auxinfopool.o gsnap_avx512-pathstorepool.o gsnap_avx512-intron.o gsnap_avx512-gbuffer.o gsnap_avx512-select64-common.o gsnap_avx512-select64-ones.o gsnap_avx512-select64-zeroes.o gsnap_avx512-ef64.o gsnap_avx512-nr-x.o gsnap_avx512-knownsplicing.o gsnap_avx512-knownindels.o gsnap_avx512-splice.o gsnap_avx512-indel.o gsnap_avx512-spliceendsgen.o gsnap_avx512-spliceends.o gsnap_avx512-bitpack64-access.o gsnap_avx512-trdiag.o gsnap_avx512-trdiagpool.o gsnap_avx512-tr-extension-search.o gsnap_avx512-univdiag.o gsnap_avx512-univdiagpool.o gsnap_avx512-sedgesort.o gsnap_avx512-auxinfo.o gsnap_avx512-pathstore.o gsnap_avx512-altsplice.o gsnap_avx512-path.o gsnap_avx512-pathpair.o gsnap_avx512-path-solve.o gsnap_avx512-path-fusion.o gsnap_avx512-path-trim.o gsnap_avx512-path-eval.o gsnap_avx512-pathpair-eval.o gsnap_avx512-path-print-alignment.o gsnap_avx512-path-print-m8.o gsnap_avx512-path-print-sam.o gsnap_avx512-path-learn.o gsnap_avx512-method.o gsnap_avx512-doublelist.o gsnap_avx512-bitvector.o gsnap_avx512-transcriptpool.o gsnap_avx512-exon.o gsnap_avx512-transcript.o gsnap_avx512-trpathpool.o gsnap_avx512-trpath.o gsnap_avx512-trpath-solve.o gsnap_avx512-trpath-convert.o gsnap_avx512-trpath-eval.o gsnap_avx512-transcriptome-search.o gsnap_avx512-vectorpool.o gsnap_avx512-repair.o gsnap_avx512-transcript-remap.o gsnap_avx512-transcript-velocity.o gsnap_avx512-intersect-small.o gsnap_avx512-intersect-uint2.o gsnap_avx512-intersect-approx-uint4.o gsnap_avx512-intersect-approx-indices-uint4.o gsnap_avx512-intersect-wdups-indices.o gsnap_avx512-intersect-lower-small.o gsnap_avx512-intersect-higher-small.o gsnap_avx512-intersect-indices-small.o gsnap_avx512-intersect-indices2-small.o gsnap_avx512-intersect-concordance-uint4.o gsnap_avx512-kmer-search.o gsnap_avx512-extension-search.o gsnap_avx512-repetitive.o gsnap_avx512-uint8table.o gsnap_avx512-uinttable.o gsnap_avx512-stage1hr.o gsnap_avx512-stage1hr-single.o gsnap_avx512-stage1hr-paired.o gsnap_avx512-uinttableuint.o gsnap_avx512-tableuint.o gsnap_avx512-single-cell.o gsnap_avx512-request.o gsnap_avx512-resulthr.o gsnap_avx512-output.o gsnap_avx512-inbuffer.o gsnap_avx512-samheader.o gsnap_avx512-printbuffer.o gsnap_avx512-outbuffer.o gsnap_avx512-uintpairtable.o gsnap_avx512-splice-count.o gsnap_avx512-support.o gsnap_avx512-datadir.o gsnap_avx512-parserange.o gsnap_avx512-getline.o gsnap_avx512-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx512 gmapl_avx512-except.o gmapl_avx512-assert.o gmapl_avx512-mem.o gmapl_avx512-intlist.o gmapl_avx512-uintlist.o gmapl_avx512-uint8list.o gmapl_avx512-list.o gmapl_avx512-littleendian.o gmapl_avx512-bigendian.o gmapl_avx512-univinterval.o gmapl_avx512-interval.o gmapl_avx512-stopwatch.o gmapl_avx512-semaphore.o gmapl_avx512-access.o gmapl_avx512-filestring.o gmapl_avx512-iit-read-univ.o gmapl_avx512-iit-read.o gmapl_avx512-md5.o gmapl_avx512-bzip2.o gmapl_avx512-fopen.o gmapl_avx512-sequence.o gmapl_avx512-reader.o gmapl_avx512-genomicpos.o gmapl_avx512-compress.o gmapl_avx512-compress-write.o gmapl_avx512-gbuffer.o gmapl_avx512-genome.o gmapl_avx512-popcount.o gmapl_avx512-dinucl_bits.o gmapl_avx512-genome_canonical.o gmapl_avx512-genome-write.o gmapl_avx512-bitpack64-read.o gmapl_avx512-bitpack64-readtwo.o gmapl_avx512-indexdb.o gmapl_avx512-oligo.o gmapl_avx512-block.o gmapl_avx512-chrom.o gmapl_avx512-segmentpos.o gmapl_avx512-chrnum.o gmapl_avx512-uinttable_rh.o gmapl_avx512-uint8table_rh.o gmapl_avx512-gregion.o gmapl_avx512-match.o gmapl_avx512-matchpool.o gmapl_avx512-diagnostic.o gmapl_avx512-stage1.o gmapl_avx512-diag.o gmapl_avx512-diagpool.o gmapl_avx512-cmet.o gmapl_avx512-atoi.o gmapl_avx512-orderstat.o gmapl_avx512-oligoindex_hr.o gmapl_avx512-intron.o gmapl_avx512-maxent.o gmapl_avx512-maxent_hr.o gmapl_avx512-pair.o gmapl_avx512-pairpool.o gmapl_avx512-cellpool.o gmapl_avx512-stage2.o gmapl_avx512-doublelist.o gmapl_avx512-smooth.o gmapl_avx512-splicestringpool.o gmapl_avx512-splicetrie_build.o gmapl_avx512-splicetrie.o gmapl_avx512-boyer-moore.o gmapl_avx512-dynprog.o gmapl_avx512-dynprog_simd.o gmapl_avx512-dynprog_single.o gmapl_avx512-dynprog_genome.o gmapl_avx512-dynprog_cdna.o gmapl_avx512-dynprog_end.o gmapl_avx512-translation.o gmapl_avx512-pbinom.o gmapl_avx512-changepoint.o gmapl_avx512-stage3.o gmapl_avx512-request.o gmapl_avx512-result.o gmapl_avx512-output.o gmapl_avx512-inbuffer.o gmapl_avx512-samheader.o gmapl_avx512-printbuffer.o gmapl_avx512-outbuffer.o gmapl_avx512-chimera.o gmapl_avx512-datadir.o gmapl_avx512-parserange.o gmapl_avx512-getline.o gmapl_avx512-gmap.o -lz -lbz2 -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx512 gsnapl_avx512-except.o gsnapl_avx512-assert.o gsnapl_avx512-mem.o gsnapl_avx512-intlist.o gsnapl_avx512-uintlist.o gsnapl_avx512-uint8list.o gsnapl_avx512-list.o gsnapl_avx512-littleendian.o gsnapl_avx512-bigendian.o gsnapl_avx512-univinterval.o gsnapl_avx512-interval.o gsnapl_avx512-stopwatch.o gsnapl_avx512-semaphore.o gsnapl_avx512-access.o gsnapl_avx512-filestring.o gsnapl_avx512-iit-read-univ.o gsnapl_avx512-iit-read.o gsnapl_avx512-bzip2.o gsnapl_avx512-reader.o gsnapl_avx512-genomicpos.o gsnapl_avx512-compress.o gsnapl_avx512-genome.o gsnapl_avx512-transcriptome.o gsnapl_avx512-popcount.o gsnapl_avx512-genomebits.o gsnapl_avx512-genomebits_consec.o gsnapl_avx512-genomebits_count.o gsnapl_avx512-genomebits_kmer.o gsnapl_avx512-genomebits_indel.o gsnapl_avx512-genomebits_decode.o gsnapl_avx512-genomebits_mismatches.o gsnapl_avx512-genomebits_trim.o gsnapl_avx512-dinucl_bits.o gsnapl_avx512-genome_sites.o gsnapl_avx512-bitpack64-read.o gsnapl_avx512-bitpack64-readtwo.o gsnapl_avx512-mergeinfo.o gsnapl_avx512-merge-diagonals-heap-uint8.o gsnapl_avx512-merge-uint8.o gsnapl_avx512-merge-diagonals-simd-uint8.o gsnapl_avx512-merge-diagonals-heap-uint4.o gsnapl_avx512-merge-uint4.o gsnapl_avx512-merge-diagonals-simd-uint4.o gsnapl_avx512-indexdb.o gsnapl_avx512-localdb-read.o gsnapl_avx512-oligo.o gsnapl_avx512-chrnum.o gsnapl_avx512-maxent_hr.o gsnapl_avx512-mapq.o gsnapl_avx512-fopen.o gsnapl_avx512-shortread.o gsnapl_avx512-junction.o gsnapl_avx512-concordance.o gsnapl_avx512-simplepair.o gsnapl_avx512-orderstat.o gsnapl_avx512-intlistpool.o gsnapl_avx512-uintlistpool.o gsnapl_avx512-uint8listpool.o gsnapl_avx512-listpool.o gsnapl_avx512-hitlistpool.o gsnapl_avx512-pathpool.o gsnapl_avx512-auxinfopool.o gsnapl_avx512-pathstorepool.o gsnapl_avx512-intron.o gsnapl_avx512-gbuffer.o gsnapl_avx512-select64-common.o gsnapl_avx512-select64-ones.o gsnapl_avx512-select64-zeroes.o gsnapl_avx512-ef64.o gsnapl_avx512-nr-x.o gsnapl_avx512-knownsplicing.o gsnapl_avx512-knownindels.o gsnapl_avx512-splice.o gsnapl_avx512-indel.o gsnapl_avx512-spliceendsgen.o gsnapl_avx512-spliceends.o gsnapl_avx512-bitpack64-access.o gsnapl_avx512-trdiag.o gsnapl_avx512-trdiagpool.o gsnapl_avx512-tr-extension-search.o gsnapl_avx512-univdiag.o gsnapl_avx512-univdiagpool.o gsnapl_avx512-sedgesort.o gsnapl_avx512-auxinfo.o gsnapl_avx512-pathstore.o gsnapl_avx512-altsplice.o gsnapl_avx512-path.o gsnapl_avx512-pathpair.o gsnapl_avx512-path-solve.o gsnapl_avx512-path-fusion.o gsnapl_avx512-path-trim.o gsnapl_avx512-path-eval.o gsnapl_avx512-pathpair-eval.o gsnapl_avx512-path-print-alignment.o gsnapl_avx512-path-print-m8.o gsnapl_avx512-path-print-sam.o gsnapl_avx512-path-learn.o gsnapl_avx512-method.o gsnapl_avx512-doublelist.o gsnapl_avx512-bitvector.o gsnapl_avx512-transcriptpool.o gsnapl_avx512-exon.o gsnapl_avx512-transcript.o gsnapl_avx512-trpathpool.o gsnapl_avx512-trpath.o gsnapl_avx512-trpath-solve.o gsnapl_avx512-trpath-convert.o gsnapl_avx512-trpath-eval.o gsnapl_avx512-transcriptome-search.o gsnapl_avx512-vectorpool.o gsnapl_avx512-repair.o gsnapl_avx512-transcript-remap.o gsnapl_avx512-transcript-velocity.o gsnapl_avx512-intersect-large.o gsnapl_avx512-intersect-small.o gsnapl_avx512-intersect-uint2.o gsnapl_avx512-intersect-approx-uint4.o gsnapl_avx512-intersect-approx-uint8.o gsnapl_avx512-intersect-approx-indices-uint8.o gsnapl_avx512-intersect-wdups-indices.o gsnapl_avx512-intersect-lower-large.o gsnapl_avx512-intersect-higher-large.o gsnapl_avx512-intersect-indices-small.o gsnapl_avx512-intersect-indices2-large.o gsnapl_avx512-intersect-indices-uint8.o gsnapl_avx512-intersect-concordance-uint8.o gsnapl_avx512-kmer-search.o gsnapl_avx512-extension-search.o gsnapl_avx512-repetitive.o gsnapl_avx512-uint8table.o gsnapl_avx512-stage1hr.o gsnapl_avx512-stage1hr-single.o gsnapl_avx512-stage1hr-paired.o gsnapl_avx512-uint8tableuint.o gsnapl_avx512-tableuint.o gsnapl_avx512-single-cell.o gsnapl_avx512-request.o gsnapl_avx512-resulthr.o gsnapl_avx512-output.o gsnapl_avx512-inbuffer.o gsnapl_avx512-samheader.o gsnapl_avx512-printbuffer.o gsnapl_avx512-outbuffer.o gsnapl_avx512-uint8pairtable.o gsnapl_avx512-splice-count.o gsnapl_avx512-support.o gsnapl_avx512-datadir.o gsnapl_avx512-parserange.o gsnapl_avx512-getline.o gsnapl_avx512-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes chmod +x md_coords chmod +x fa_coords chmod +x psl_splicesites chmod +x psl_introns cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x psl_genes cp gtf_genes.pl gtf_genes chmod +x ensembl_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns cp gff3_genes.pl gff3_genes chmod +x gtf_splicesites chmod +x gtf_introns chmod +x gtf_genes cp dbsnp_iit.pl dbsnp_iit chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites chmod +x gff3_introns cp gvf_iit.pl gvf_iit chmod +x gff3_genes cp vcf_iit.pl vcf_iit chmod +x dbsnp_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_test --no-parallel cd build && make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making check in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' Making check in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making check in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make check-TESTS make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[5]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' PASS: align.test PASS: coords1.test PASS: setup1.test PASS: iit.test ============================================================================ Testsuite summary for gmap 2024-11-20 ============================================================================ # TOTAL: 4 # PASS: 4 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--builddir=build dh_prep -O--builddir=build debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' mkdir -p /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Genomic Mapping and Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gmap |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Genomic Short-read Nucleotide Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gsnap |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gsnap.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Large Genome Mapping and Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gmapl |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmapl.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Large Genome Short-read Nucleotide Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gsnapl |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gsnapl.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Tool for genome database creation for GMAP or GSNAP' \ /build/reproducible-path/gmap-2024-11-20+ds/build/util/gmap_build |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap_build.1 dh_auto_install --builddir build_avx512 cd build_avx512 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx512 gmapl.avx512 gsnap.avx512 gsnapl.avx512 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' dh_auto_install --builddir build_avx2 cd build_avx2 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx2 gmapl.avx2 gsnap.avx2 gsnapl.avx2 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' dh_auto_install --builddir build_sse42 cd build_sse42 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse42 gmapl.sse42 gsnap.sse42 gsnapl.sse42 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' dh_auto_install --builddir build_sse41 cd build_sse41 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse41 gmapl.sse41 gsnap.sse41 gsnapl.sse41 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' dh_auto_install --builddir build_ssse3 cd build_ssse3 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.ssse3 gmapl.ssse3 gsnap.ssse3 gsnapl.ssse3 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' dh_auto_install cd build && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse2 gmapl.sse2 gsnap.sse2 gsnapl.sse2 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' mkdir -p debian/gmap/usr/bin dh_install for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \ cd /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap/; \ ls -1 gmap*.* gsnap*.* `; do \ ln -s /usr/lib/gmap/$bin debian/gmap/usr/bin/$bin; \ done make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_installdocs -O--builddir=build dh_installchangelogs -O--builddir=build debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' mkdir /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/doc/gmap/examples find tests/ -type f -print0 | xargs -0r sed -i \ -e 's@/build/reproducible-path/gmap-2024-11-20+ds@«buildpath»@g' \ -e 's@\#! /bin/bash@\#! /bin/sh@g' tar --sort=name \ --mtime="@1740521462" \ --owner=root --group=root --numeric-owner \ --mode=go=rX,u+rw,a-s \ --exclude='*/align.log' \ --exclude='*/Makefile' \ --exclude='*/Makefile.in' \ -cJf /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/doc/gmap/examples/tests.tar.xz tests make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_installman -O--builddir=build dh_installsystemduser -O--builddir=build dh_lintian -O--builddir=build dh_perl -O--builddir=build dh_link -O--builddir=build dh_strip_nondeterminism -O--builddir=build dh_compress -O--builddir=build dh_fixperms -O--builddir=build dh_missing -O--builddir=build dh_dwz -a -O--builddir=build dh_strip -a -O--builddir=build dh_makeshlibs -a -O--builddir=build dh_shlibdeps -a -O--builddir=build dh_installdeb -O--builddir=build dh_gencontrol -O--builddir=build dh_md5sums -O--builddir=build dh_builddeb -O--builddir=build dpkg-deb: building package 'gmap' in '../gmap_2024-11-20+ds-2_amd64.deb'. dpkg-deb: building package 'gmap-dbgsym' in '../gmap-dbgsym_2024-11-20+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gmap_2024-11-20+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gmap_2024-11-20+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2740700 and its subdirectories I: Current time: Wed Oct 21 09:21:56 -12 2026 I: pbuilder-time-stamp: 1792617716 Wed Oct 21 21:21:56 UTC 2026 I: Signing ./b1/gmap_2024-11-20+ds-2_amd64.buildinfo as gmap_2024-11-20+ds-2_amd64.buildinfo.asc Wed Oct 21 21:21:56 UTC 2026 I: Signed ./b1/gmap_2024-11-20+ds-2_amd64.buildinfo as ./b1/gmap_2024-11-20+ds-2_amd64.buildinfo.asc Wed Oct 21 21:21:56 UTC 2026 - build #1 for gmap/forky/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Wed Oct 21 21:21:56 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-045TjmKe, removing. /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 14:58 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 14:47 b2 -rw-rw-r-- 1 jenkins jenkins 2309 Feb 25 2025 gmap_2024-11-20+ds-2.dsc -rw------- 1 jenkins jenkins 3423 Sep 18 14:47 rbuildlog.1Yuep4q /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b1: total 98040 -rw-r--r-- 1 jenkins jenkins 8143318 Sep 18 14:58 build.log -rw-r--r-- 1 jenkins jenkins 55899988 Sep 18 14:58 gmap-dbgsym_2024-11-20+ds-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 14076 Sep 18 14:58 gmap_2024-11-20+ds-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2309 Sep 18 14:58 gmap_2024-11-20+ds-2.dsc -rw-r--r-- 1 jenkins jenkins 5090 Sep 18 14:58 gmap_2024-11-20+ds-2_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5972 Sep 18 14:58 gmap_2024-11-20+ds-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1509 Sep 18 14:58 gmap_2024-11-20+ds-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 36295460 Sep 18 14:58 gmap_2024-11-20+ds-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1352 Sep 18 14:58 gmap_2024-11-20+ds-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b2: total 0 Thu Sep 18 14:58:57 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 21 09:10:58 -12 2026 I: pbuilder-time-stamp: 1792617058 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gmap_2024-11-20+ds-2.dsc] I: copying [./gmap_2024-11-20+ds.orig.tar.xz] I: copying [./gmap_2024-11-20+ds-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gmap_2024-11-20+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting gmap in gmap-2024-11-20+ds dpkg-source: info: unpacking gmap_2024-11-20+ds.orig.tar.xz dpkg-source: info: unpacking gmap_2024-11-20+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying install-data-local dpkg-source: info: applying remove_getopt_code_copy.patch dpkg-source: info: applying simd_fixes dpkg-source: info: applying c23.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2740700/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d85274bf58c74458a9c9761240c5f1a7' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2740700' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/pbuilderrc_sc0r --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b1 --logfile b1/build.log gmap_2024-11-20+ds-2.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2740700/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), architecture-is-little-endian, help2man, libbz2-dev, zlib1g-dev, debhelper, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 12.9 MB of archives. After unpacking 53.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get: 13 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 24 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 help2man amd64 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 12.9 MB in 0s (121 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package architecture-properties:amd64. Preparing to unpack .../11-architecture-properties_0.2.6_amd64.deb ... Unpacking architecture-properties:amd64 (0.2.6) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20240727.1_all.deb ... 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Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../23-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../25-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../26-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package help2man. Preparing to unpack .../31-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../32-libbz2-dev_1.0.8-6_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-6) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../33-libsimde-dev_0.8.2-3_all.deb ... Unpacking libsimde-dev (0.8.2-3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../34-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:amd64 (0.2.6) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gmap-2024-11-20+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gmap_2024-11-20+ds-2_source.changes dpkg-buildpackage: info: source package gmap dpkg-buildpackage: info: source version 2024-11-20+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --builddir build debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_clean --builddir build_avx512 dh_auto_clean --builddir build_avx2 dh_auto_clean --builddir build_sse42 dh_auto_clean --builddir build_sse41 dh_auto_clean --builddir build_ssse3 dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_autoreconf_clean -O--builddir=build dh_clean -O--builddir=build debian/rules binary dh binary --builddir build dh_update_autotools_config -O--builddir=build dh_autoreconf -O--builddir=build configure.ac:104: installing 'config/compile' configure.ac:85: installing 'config/config.guess' configure.ac:85: installing 'config/config.sub' configure.ac:109: installing 'config/install-sh' configure.ac:109: installing 'config/missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing 'config/depcomp' src/Makefile.am:870: warning: variable 'dist_compare2truth_SOURCES' is defined but no program or src/Makefile.am:870: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1216: warning: variable 'dist_gcount_bulk_SOURCES' is defined but no program or src/Makefile.am:1216: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1242: warning: variable 'dist_gcount_sc_SOURCES' is defined but no program or src/Makefile.am:1242: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:216: warning: variable 'dist_gexact_SOURCES' is defined but no program or src/Makefile.am:216: library has 'gexact' as canonical name (possible typo) src/Makefile.am:742: warning: variable 'dist_gexact_arm_SOURCES' is defined but no program or src/Makefile.am:742: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:772: warning: variable 'dist_gexact_avx2_SOURCES' is defined but no program or src/Makefile.am:772: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:778: warning: variable 'dist_gexact_avx512_SOURCES' is defined but no program or src/Makefile.am:778: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:784: warning: variable 'dist_gexact_avx512bw_SOURCES' is defined but no program or src/Makefile.am:784: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:736: warning: variable 'dist_gexact_nosimd_SOURCES' is defined but no program or src/Makefile.am:736: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:748: warning: variable 'dist_gexact_sse2_SOURCES' is defined but no program or src/Makefile.am:748: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:760: warning: variable 'dist_gexact_sse41_SOURCES' is defined but no program or src/Makefile.am:760: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:766: warning: variable 'dist_gexact_sse42_SOURCES' is defined but no program or src/Makefile.am:766: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:754: warning: variable 'dist_gexact_ssse3_SOURCES' is defined but no program or src/Makefile.am:754: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:223: warning: variable 'dist_gfilter_SOURCES' is defined but no program or src/Makefile.am:223: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:816: warning: variable 'dist_gfilter_arm_SOURCES' is defined but no program or src/Makefile.am:816: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:846: warning: variable 'dist_gfilter_avx2_SOURCES' is defined but no program or src/Makefile.am:846: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:852: warning: variable 'dist_gfilter_avx512_SOURCES' is defined but no program or src/Makefile.am:852: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:858: warning: variable 'dist_gfilter_avx512bw_SOURCES' is defined but no program or src/Makefile.am:858: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:810: warning: variable 'dist_gfilter_nosimd_SOURCES' is defined but no program or src/Makefile.am:810: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:822: warning: variable 'dist_gfilter_sse2_SOURCES' is defined but no program or src/Makefile.am:822: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:834: warning: variable 'dist_gfilter_sse41_SOURCES' is defined but no program or src/Makefile.am:834: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:840: warning: variable 'dist_gfilter_sse42_SOURCES' is defined but no program or src/Makefile.am:840: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:828: warning: variable 'dist_gfilter_ssse3_SOURCES' is defined but no program or src/Makefile.am:828: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1132: warning: variable 'dist_iit_pileup_SOURCES' is defined but no program or src/Makefile.am:1132: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1154: warning: variable 'dist_sam_sort_SOURCES' is defined but no program or src/Makefile.am:1154: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1172: warning: variable 'dist_umi_correct_SOURCES' is defined but no program or src/Makefile.am:1172: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1191: warning: variable 'dist_velocity_counts_SOURCES' is defined but no program or src/Makefile.am:1191: library has 'velocity_counts' as canonical name (possible typo) src/Makefile.am:869: warning: variable 'compare2truth_LDADD' is defined but no program or src/Makefile.am:869: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1215: warning: variable 'gcount_bulk_LDADD' is defined but no program or src/Makefile.am:1215: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1241: warning: variable 'gcount_sc_LDADD' is defined but no program or src/Makefile.am:1241: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:215: warning: variable 'gexact_LDADD' is defined but no program or src/Makefile.am:215: library has 'gexact' as canonical name (possible typo) src/Makefile.am:741: warning: variable 'gexact_arm_LDADD' is defined but no program or src/Makefile.am:741: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:771: warning: variable 'gexact_avx2_LDADD' is defined but no program or src/Makefile.am:771: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:777: warning: variable 'gexact_avx512_LDADD' is defined but no program or src/Makefile.am:777: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:783: warning: variable 'gexact_avx512bw_LDADD' is defined but no program or src/Makefile.am:783: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:735: warning: variable 'gexact_nosimd_LDADD' is defined but no program or src/Makefile.am:735: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:747: warning: variable 'gexact_sse2_LDADD' is defined but no program or src/Makefile.am:747: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:759: warning: variable 'gexact_sse41_LDADD' is defined but no program or src/Makefile.am:759: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:765: warning: variable 'gexact_sse42_LDADD' is defined but no program or src/Makefile.am:765: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:753: warning: variable 'gexact_ssse3_LDADD' is defined but no program or src/Makefile.am:753: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:222: warning: variable 'gfilter_LDADD' is defined but no program or src/Makefile.am:222: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:815: warning: variable 'gfilter_arm_LDADD' is defined but no program or src/Makefile.am:815: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:845: warning: variable 'gfilter_avx2_LDADD' is defined but no program or src/Makefile.am:845: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:851: warning: variable 'gfilter_avx512_LDADD' is defined but no program or src/Makefile.am:851: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:857: warning: variable 'gfilter_avx512bw_LDADD' is defined but no program or src/Makefile.am:857: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:809: warning: variable 'gfilter_nosimd_LDADD' is defined but no program or src/Makefile.am:809: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:821: warning: variable 'gfilter_sse2_LDADD' is defined but no program or src/Makefile.am:821: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:833: warning: variable 'gfilter_sse41_LDADD' is defined but no program or src/Makefile.am:833: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:839: warning: variable 'gfilter_sse42_LDADD' is defined but no program or src/Makefile.am:839: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:827: warning: variable 'gfilter_ssse3_LDADD' is defined but no program or src/Makefile.am:827: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1131: warning: variable 'iit_pileup_LDADD' is defined but no program or src/Makefile.am:1131: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1153: warning: variable 'sam_sort_LDADD' is defined but no program or src/Makefile.am:1153: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1171: warning: variable 'umi_correct_LDADD' is defined but no program or src/Makefile.am:1171: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1190: warning: variable 'velocity_counts_LDADD' is defined but no program or src/Makefile.am:1190: library has 'velocity_counts' as canonical name (possible typo) src/Makefile.am:868: warning: variable 'compare2truth_LDFLAGS' is defined but no program or src/Makefile.am:868: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1214: warning: variable 'gcount_bulk_LDFLAGS' is defined but no program or src/Makefile.am:1214: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1240: warning: variable 'gcount_sc_LDFLAGS' is defined but no program or src/Makefile.am:1240: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:214: warning: variable 'gexact_LDFLAGS' is defined but no program or src/Makefile.am:214: library has 'gexact' as canonical name (possible typo) src/Makefile.am:740: warning: variable 'gexact_arm_LDFLAGS' is defined but no program or src/Makefile.am:740: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:770: warning: variable 'gexact_avx2_LDFLAGS' is defined but no program or src/Makefile.am:770: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:776: warning: variable 'gexact_avx512_LDFLAGS' is defined but no program or src/Makefile.am:776: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:782: warning: variable 'gexact_avx512bw_LDFLAGS' is defined but no program or src/Makefile.am:782: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:734: warning: variable 'gexact_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:734: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:746: warning: variable 'gexact_sse2_LDFLAGS' is defined but no program or src/Makefile.am:746: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:758: warning: variable 'gexact_sse41_LDFLAGS' is defined but no program or src/Makefile.am:758: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:764: warning: variable 'gexact_sse42_LDFLAGS' is defined but no program or src/Makefile.am:764: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:752: warning: variable 'gexact_ssse3_LDFLAGS' is defined but no program or src/Makefile.am:752: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:221: warning: variable 'gfilter_LDFLAGS' is defined but no program or src/Makefile.am:221: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:814: warning: variable 'gfilter_arm_LDFLAGS' is defined but no program or src/Makefile.am:814: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:844: warning: variable 'gfilter_avx2_LDFLAGS' is defined but no program or src/Makefile.am:844: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:850: warning: variable 'gfilter_avx512_LDFLAGS' is defined but no program or src/Makefile.am:850: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:856: warning: variable 'gfilter_avx512bw_LDFLAGS' is defined but no program or src/Makefile.am:856: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:808: warning: variable 'gfilter_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:808: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:820: warning: variable 'gfilter_sse2_LDFLAGS' is defined but no program or src/Makefile.am:820: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:832: warning: variable 'gfilter_sse41_LDFLAGS' is defined but no program or src/Makefile.am:832: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:838: warning: variable 'gfilter_sse42_LDFLAGS' is defined but no program or src/Makefile.am:838: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:826: warning: variable 'gfilter_ssse3_LDFLAGS' is defined but no program or src/Makefile.am:826: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1130: warning: variable 'iit_pileup_LDFLAGS' is defined but no program or src/Makefile.am:1130: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1152: warning: variable 'sam_sort_LDFLAGS' is defined but no program or src/Makefile.am:1152: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1170: warning: variable 'umi_correct_LDFLAGS' is defined but no program or src/Makefile.am:1170: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1189: warning: variable 'velocity_counts_LDFLAGS' is defined but no program or src/Makefile.am:1189: library has 'velocity_counts' as canonical name (possible typo) parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' rm -Rf src/simde DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI" dh_auto_configure --reload-all-buildenv-variables -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2 cd build && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2 checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse2 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse2 checking SSE2 compiler flags to be used... -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI" dh_auto_configure --reload-all-buildenv-variables --builddir build_ssse3 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=ssse3 ax_cv_cpu_has_ssse3_ext=yes ax_cv_compile_ssse3_ext=yes ax_cv_link_tmmintrin_h=yes cd build_ssse3 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=ssse3 ax_cv_cpu_has_ssse3_ext=yes ax_cv_compile_ssse3_ext=yes ax_cv_link_tmmintrin_h=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... ssse3 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... ssse3 checking SSSE3 compiler flags to be used... -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_STTNI" dh_auto_configure --builddir build_sse41 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse41 ax_cv_cpu_has_sse41_ext=yes ax_cv_compile_sse41_ext=yes ax_cv_link_smmintrin_h=yes cd build_sse41 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse41 ax_cv_cpu_has_sse41_ext=yes ax_cv_compile_sse41_ext=yes ax_cv_link_smmintrin_h=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse41 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse41 checking SSE4.1 compiler flags to be used... -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 dh_auto_configure --builddir build_sse42 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse42 ax_cv_cpu_has_sse42_ext=yes ax_cv_compile_sse42_ext=yes ax_cv_link_nmmintrin_h=yes ax_cv_cpu_has_popcnt_ext=yes ax_make_sse42=yes ax_cv_cpu_has_bmi1_ext=yes ax_cv_compile_bmi_ext=yes ax_cv_link_bmi=yes cd build_sse42 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse42 ax_cv_cpu_has_sse42_ext=yes ax_cv_compile_sse42_ext=yes ax_cv_link_nmmintrin_h=yes ax_cv_cpu_has_popcnt_ext=yes ax_make_sse42=yes ax_cv_cpu_has_bmi1_ext=yes ax_cv_compile_bmi_ext=yes ax_cv_link_bmi=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm... yes checking for abm linker support... yes checking for _popcnt32 run support... yes checking for _lzcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi... yes checking for bmi linker support... yes checking for _tzcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse42 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse42 checking SSE4.2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 dh_auto_configure --builddir build_avx2 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx2 ax_make_avx2=yes ax_cv_cpu_has_bmi2_ext=yes ax_cv_compile_bmi2_ext=yes ax_cv_link_bmi2=yes cd build_avx2 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx2 ax_make_avx2=yes ax_cv_cpu_has_bmi2_ext=yes ax_cv_compile_bmi2_ext=yes ax_cv_link_bmi2=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2... yes checking for bmi2 linker support... yes checking for _pext run support... yes checking for user-selected SIMD level... avx2 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... avx2 checking AVX2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 dh_auto_configure --builddir build_avx512 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx512 ax_cv_cpu_has_avx512_ext=yes ax_cv_compile_avx512_ext=yes ax_cv_compile_avx512bw_ext=no ax_cv_link_avx512bw=no cd build_avx512 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx512 ax_cv_cpu_has_avx512_ext=yes ax_cv_compile_avx512_ext=yes ax_cv_compile_avx512bw_ext=no ax_cv_link_avx512bw=no checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd... yes checking for nmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw... yes checking for avx512vl and avx512bw linker support... yes checking for user-selected SIMD level... avx512 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... avx512 checking AVX512 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw # skipping avx512bw for now: # ../../src/oligoindex_hr.c: In function 'count_positions_fwd_simd': make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_build cd build && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read.c: In function 'IIT_debug': In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/iit-read-univ.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.sse2 gmap_sse2-except.o gmap_sse2-assert.o gmap_sse2-mem.o gmap_sse2-intlist.o gmap_sse2-uintlist.o gmap_sse2-list.o gmap_sse2-littleendian.o gmap_sse2-bigendian.o gmap_sse2-univinterval.o gmap_sse2-interval.o gmap_sse2-stopwatch.o gmap_sse2-semaphore.o gmap_sse2-access.o gmap_sse2-filestring.o gmap_sse2-iit-read-univ.o gmap_sse2-iit-read.o gmap_sse2-md5.o gmap_sse2-bzip2.o gmap_sse2-fopen.o gmap_sse2-sequence.o gmap_sse2-reader.o gmap_sse2-genomicpos.o gmap_sse2-compress.o gmap_sse2-compress-write.o gmap_sse2-gbuffer.o gmap_sse2-genome.o gmap_sse2-popcount.o gmap_sse2-dinucl_bits.o gmap_sse2-genome_canonical.o gmap_sse2-genome-write.o gmap_sse2-bitpack64-read.o gmap_sse2-bitpack64-readtwo.o gmap_sse2-indexdb.o gmap_sse2-oligo.o gmap_sse2-block.o gmap_sse2-chrom.o gmap_sse2-segmentpos.o gmap_sse2-chrnum.o gmap_sse2-uinttable_rh.o gmap_sse2-gregion.o gmap_sse2-match.o gmap_sse2-matchpool.o gmap_sse2-diagnostic.o gmap_sse2-stage1.o gmap_sse2-diag.o gmap_sse2-diagpool.o gmap_sse2-cmet.o gmap_sse2-atoi.o gmap_sse2-orderstat.o gmap_sse2-oligoindex_hr.o gmap_sse2-intron.o gmap_sse2-maxent.o gmap_sse2-maxent_hr.o gmap_sse2-pair.o gmap_sse2-pairpool.o gmap_sse2-cellpool.o gmap_sse2-stage2.o gmap_sse2-doublelist.o gmap_sse2-smooth.o gmap_sse2-splicestringpool.o gmap_sse2-splicetrie_build.o gmap_sse2-splicetrie.o gmap_sse2-boyer-moore.o gmap_sse2-dynprog.o gmap_sse2-dynprog_simd.o gmap_sse2-dynprog_single.o gmap_sse2-dynprog_genome.o gmap_sse2-dynprog_cdna.o gmap_sse2-dynprog_end.o gmap_sse2-translation.o gmap_sse2-pbinom.o gmap_sse2-changepoint.o gmap_sse2-stage3.o gmap_sse2-request.o gmap_sse2-result.o gmap_sse2-output.o gmap_sse2-inbuffer.o gmap_sse2-samheader.o gmap_sse2-printbuffer.o gmap_sse2-outbuffer.o gmap_sse2-chimera.o gmap_sse2-datadir.o gmap_sse2-parserange.o gmap_sse2-getline.o gmap_sse2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.sse2 gmapl_sse2-except.o gmapl_sse2-assert.o gmapl_sse2-mem.o gmapl_sse2-intlist.o gmapl_sse2-uintlist.o gmapl_sse2-uint8list.o gmapl_sse2-list.o gmapl_sse2-littleendian.o gmapl_sse2-bigendian.o gmapl_sse2-univinterval.o gmapl_sse2-interval.o gmapl_sse2-stopwatch.o gmapl_sse2-semaphore.o gmapl_sse2-access.o gmapl_sse2-filestring.o gmapl_sse2-iit-read-univ.o gmapl_sse2-iit-read.o gmapl_sse2-md5.o gmapl_sse2-bzip2.o gmapl_sse2-fopen.o gmapl_sse2-sequence.o gmapl_sse2-reader.o gmapl_sse2-genomicpos.o gmapl_sse2-compress.o gmapl_sse2-compress-write.o gmapl_sse2-gbuffer.o gmapl_sse2-genome.o gmapl_sse2-popcount.o gmapl_sse2-dinucl_bits.o gmapl_sse2-genome_canonical.o gmapl_sse2-genome-write.o gmapl_sse2-bitpack64-read.o gmapl_sse2-bitpack64-readtwo.o gmapl_sse2-indexdb.o gmapl_sse2-oligo.o gmapl_sse2-block.o gmapl_sse2-chrom.o gmapl_sse2-segmentpos.o gmapl_sse2-chrnum.o gmapl_sse2-uinttable_rh.o gmapl_sse2-uint8table_rh.o gmapl_sse2-gregion.o gmapl_sse2-match.o gmapl_sse2-matchpool.o gmapl_sse2-diagnostic.o gmapl_sse2-stage1.o gmapl_sse2-diag.o gmapl_sse2-diagpool.o gmapl_sse2-cmet.o gmapl_sse2-atoi.o gmapl_sse2-orderstat.o gmapl_sse2-oligoindex_hr.o gmapl_sse2-intron.o gmapl_sse2-maxent.o gmapl_sse2-maxent_hr.o gmapl_sse2-pair.o gmapl_sse2-pairpool.o gmapl_sse2-cellpool.o gmapl_sse2-stage2.o gmapl_sse2-doublelist.o gmapl_sse2-smooth.o gmapl_sse2-splicestringpool.o gmapl_sse2-splicetrie_build.o gmapl_sse2-splicetrie.o gmapl_sse2-boyer-moore.o gmapl_sse2-dynprog.o gmapl_sse2-dynprog_simd.o gmapl_sse2-dynprog_single.o gmapl_sse2-dynprog_genome.o gmapl_sse2-dynprog_cdna.o gmapl_sse2-dynprog_end.o gmapl_sse2-translation.o gmapl_sse2-pbinom.o gmapl_sse2-changepoint.o gmapl_sse2-stage3.o gmapl_sse2-request.o gmapl_sse2-result.o gmapl_sse2-output.o gmapl_sse2-inbuffer.o gmapl_sse2-samheader.o gmapl_sse2-printbuffer.o gmapl_sse2-outbuffer.o gmapl_sse2-chimera.o gmapl_sse2-datadir.o gmapl_sse2-parserange.o gmapl_sse2-getline.o gmapl_sse2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.sse2 gsnap_sse2-except.o gsnap_sse2-assert.o gsnap_sse2-mem.o gsnap_sse2-intlist.o gsnap_sse2-uintlist.o gsnap_sse2-list.o gsnap_sse2-littleendian.o gsnap_sse2-bigendian.o gsnap_sse2-univinterval.o gsnap_sse2-interval.o gsnap_sse2-stopwatch.o gsnap_sse2-semaphore.o gsnap_sse2-access.o gsnap_sse2-filestring.o gsnap_sse2-iit-read-univ.o gsnap_sse2-iit-read.o gsnap_sse2-bzip2.o gsnap_sse2-reader.o gsnap_sse2-genomicpos.o gsnap_sse2-compress.o gsnap_sse2-genome.o gsnap_sse2-transcriptome.o gsnap_sse2-popcount.o gsnap_sse2-genomebits.o gsnap_sse2-genomebits_consec.o gsnap_sse2-genomebits_count.o gsnap_sse2-genomebits_kmer.o gsnap_sse2-genomebits_indel.o gsnap_sse2-genomebits_decode.o gsnap_sse2-genomebits_mismatches.o gsnap_sse2-genomebits_trim.o gsnap_sse2-dinucl_bits.o gsnap_sse2-genome_sites.o gsnap_sse2-bitpack64-read.o gsnap_sse2-bitpack64-readtwo.o gsnap_sse2-mergeinfo.o gsnap_sse2-merge-diagonals-heap-uint4.o gsnap_sse2-merge-uint4.o gsnap_sse2-merge-diagonals-simd-uint4.o gsnap_sse2-indexdb.o gsnap_sse2-localdb-read.o gsnap_sse2-oligo.o gsnap_sse2-chrnum.o gsnap_sse2-maxent_hr.o gsnap_sse2-mapq.o gsnap_sse2-fopen.o gsnap_sse2-shortread.o gsnap_sse2-junction.o gsnap_sse2-concordance.o gsnap_sse2-simplepair.o gsnap_sse2-orderstat.o gsnap_sse2-intlistpool.o gsnap_sse2-uintlistpool.o gsnap_sse2-listpool.o gsnap_sse2-hitlistpool.o gsnap_sse2-pathpool.o gsnap_sse2-auxinfopool.o gsnap_sse2-pathstorepool.o gsnap_sse2-intron.o gsnap_sse2-gbuffer.o gsnap_sse2-select64-common.o gsnap_sse2-select64-ones.o gsnap_sse2-select64-zeroes.o gsnap_sse2-ef64.o gsnap_sse2-nr-x.o gsnap_sse2-knownsplicing.o gsnap_sse2-knownindels.o gsnap_sse2-splice.o gsnap_sse2-indel.o gsnap_sse2-spliceendsgen.o gsnap_sse2-spliceends.o gsnap_sse2-bitpack64-access.o gsnap_sse2-trdiag.o gsnap_sse2-trdiagpool.o gsnap_sse2-tr-extension-search.o gsnap_sse2-univdiag.o gsnap_sse2-univdiagpool.o gsnap_sse2-sedgesort.o gsnap_sse2-auxinfo.o gsnap_sse2-pathstore.o gsnap_sse2-altsplice.o gsnap_sse2-path.o gsnap_sse2-pathpair.o gsnap_sse2-path-solve.o gsnap_sse2-path-fusion.o gsnap_sse2-path-trim.o gsnap_sse2-path-eval.o gsnap_sse2-pathpair-eval.o gsnap_sse2-path-print-alignment.o gsnap_sse2-path-print-m8.o gsnap_sse2-path-print-sam.o gsnap_sse2-path-learn.o gsnap_sse2-method.o gsnap_sse2-doublelist.o gsnap_sse2-bitvector.o gsnap_sse2-transcriptpool.o gsnap_sse2-exon.o gsnap_sse2-transcript.o gsnap_sse2-trpathpool.o gsnap_sse2-trpath.o gsnap_sse2-trpath-solve.o gsnap_sse2-trpath-convert.o gsnap_sse2-trpath-eval.o gsnap_sse2-transcriptome-search.o gsnap_sse2-vectorpool.o gsnap_sse2-repair.o gsnap_sse2-transcript-remap.o gsnap_sse2-transcript-velocity.o gsnap_sse2-intersect-small.o gsnap_sse2-intersect-uint2.o gsnap_sse2-intersect-approx-uint4.o gsnap_sse2-intersect-approx-indices-uint4.o gsnap_sse2-intersect-wdups-indices.o gsnap_sse2-intersect-lower-small.o gsnap_sse2-intersect-higher-small.o gsnap_sse2-intersect-indices-small.o gsnap_sse2-intersect-indices2-small.o gsnap_sse2-intersect-concordance-uint4.o gsnap_sse2-kmer-search.o gsnap_sse2-extension-search.o gsnap_sse2-repetitive.o gsnap_sse2-uint8table.o gsnap_sse2-uinttable.o gsnap_sse2-stage1hr.o gsnap_sse2-stage1hr-single.o gsnap_sse2-stage1hr-paired.o gsnap_sse2-uinttableuint.o gsnap_sse2-tableuint.o gsnap_sse2-single-cell.o gsnap_sse2-request.o gsnap_sse2-resulthr.o gsnap_sse2-output.o gsnap_sse2-inbuffer.o gsnap_sse2-samheader.o gsnap_sse2-printbuffer.o gsnap_sse2-outbuffer.o gsnap_sse2-uintpairtable.o gsnap_sse2-splice-count.o gsnap_sse2-support.o gsnap_sse2-datadir.o gsnap_sse2-parserange.o gsnap_sse2-getline.o gsnap_sse2-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.sse2 gsnapl_sse2-except.o gsnapl_sse2-assert.o gsnapl_sse2-mem.o gsnapl_sse2-intlist.o gsnapl_sse2-uintlist.o gsnapl_sse2-uint8list.o gsnapl_sse2-list.o gsnapl_sse2-littleendian.o gsnapl_sse2-bigendian.o gsnapl_sse2-univinterval.o gsnapl_sse2-interval.o gsnapl_sse2-stopwatch.o gsnapl_sse2-semaphore.o gsnapl_sse2-access.o gsnapl_sse2-filestring.o gsnapl_sse2-iit-read-univ.o gsnapl_sse2-iit-read.o gsnapl_sse2-bzip2.o gsnapl_sse2-reader.o gsnapl_sse2-genomicpos.o gsnapl_sse2-compress.o gsnapl_sse2-genome.o gsnapl_sse2-transcriptome.o gsnapl_sse2-popcount.o gsnapl_sse2-genomebits.o gsnapl_sse2-genomebits_consec.o gsnapl_sse2-genomebits_count.o gsnapl_sse2-genomebits_kmer.o gsnapl_sse2-genomebits_indel.o gsnapl_sse2-genomebits_decode.o gsnapl_sse2-genomebits_mismatches.o gsnapl_sse2-genomebits_trim.o gsnapl_sse2-dinucl_bits.o gsnapl_sse2-genome_sites.o gsnapl_sse2-bitpack64-read.o gsnapl_sse2-bitpack64-readtwo.o gsnapl_sse2-mergeinfo.o gsnapl_sse2-merge-diagonals-heap-uint8.o gsnapl_sse2-merge-uint8.o gsnapl_sse2-merge-diagonals-simd-uint8.o gsnapl_sse2-merge-diagonals-heap-uint4.o gsnapl_sse2-merge-uint4.o gsnapl_sse2-merge-diagonals-simd-uint4.o gsnapl_sse2-indexdb.o gsnapl_sse2-localdb-read.o gsnapl_sse2-oligo.o gsnapl_sse2-chrnum.o gsnapl_sse2-maxent_hr.o gsnapl_sse2-mapq.o gsnapl_sse2-fopen.o gsnapl_sse2-shortread.o gsnapl_sse2-junction.o gsnapl_sse2-concordance.o gsnapl_sse2-simplepair.o gsnapl_sse2-orderstat.o gsnapl_sse2-intlistpool.o gsnapl_sse2-uintlistpool.o gsnapl_sse2-uint8listpool.o gsnapl_sse2-listpool.o gsnapl_sse2-hitlistpool.o gsnapl_sse2-pathpool.o gsnapl_sse2-auxinfopool.o gsnapl_sse2-pathstorepool.o gsnapl_sse2-intron.o gsnapl_sse2-gbuffer.o gsnapl_sse2-select64-common.o gsnapl_sse2-select64-ones.o gsnapl_sse2-select64-zeroes.o gsnapl_sse2-ef64.o gsnapl_sse2-nr-x.o gsnapl_sse2-knownsplicing.o gsnapl_sse2-knownindels.o gsnapl_sse2-splice.o gsnapl_sse2-indel.o gsnapl_sse2-spliceendsgen.o gsnapl_sse2-spliceends.o gsnapl_sse2-bitpack64-access.o gsnapl_sse2-trdiag.o gsnapl_sse2-trdiagpool.o gsnapl_sse2-tr-extension-search.o gsnapl_sse2-univdiag.o gsnapl_sse2-univdiagpool.o gsnapl_sse2-sedgesort.o gsnapl_sse2-auxinfo.o gsnapl_sse2-pathstore.o gsnapl_sse2-altsplice.o gsnapl_sse2-path.o gsnapl_sse2-pathpair.o gsnapl_sse2-path-solve.o gsnapl_sse2-path-fusion.o gsnapl_sse2-path-trim.o gsnapl_sse2-path-eval.o gsnapl_sse2-pathpair-eval.o gsnapl_sse2-path-print-alignment.o gsnapl_sse2-path-print-m8.o gsnapl_sse2-path-print-sam.o gsnapl_sse2-path-learn.o gsnapl_sse2-method.o gsnapl_sse2-doublelist.o gsnapl_sse2-bitvector.o gsnapl_sse2-transcriptpool.o gsnapl_sse2-exon.o gsnapl_sse2-transcript.o gsnapl_sse2-trpathpool.o gsnapl_sse2-trpath.o gsnapl_sse2-trpath-solve.o gsnapl_sse2-trpath-convert.o gsnapl_sse2-trpath-eval.o gsnapl_sse2-transcriptome-search.o gsnapl_sse2-vectorpool.o gsnapl_sse2-repair.o gsnapl_sse2-transcript-remap.o gsnapl_sse2-transcript-velocity.o gsnapl_sse2-intersect-large.o gsnapl_sse2-intersect-small.o gsnapl_sse2-intersect-uint2.o gsnapl_sse2-intersect-approx-uint4.o gsnapl_sse2-intersect-approx-uint8.o gsnapl_sse2-intersect-approx-indices-uint8.o gsnapl_sse2-intersect-wdups-indices.o gsnapl_sse2-intersect-lower-large.o gsnapl_sse2-intersect-higher-large.o gsnapl_sse2-intersect-indices-small.o gsnapl_sse2-intersect-indices2-large.o gsnapl_sse2-intersect-indices-uint8.o gsnapl_sse2-intersect-concordance-uint8.o gsnapl_sse2-kmer-search.o gsnapl_sse2-extension-search.o gsnapl_sse2-repetitive.o gsnapl_sse2-uint8table.o gsnapl_sse2-stage1hr.o gsnapl_sse2-stage1hr-single.o gsnapl_sse2-stage1hr-paired.o gsnapl_sse2-uint8tableuint.o gsnapl_sse2-tableuint.o gsnapl_sse2-single-cell.o gsnapl_sse2-request.o gsnapl_sse2-resulthr.o gsnapl_sse2-output.o gsnapl_sse2-inbuffer.o gsnapl_sse2-samheader.o gsnapl_sse2-printbuffer.o gsnapl_sse2-outbuffer.o gsnapl_sse2-uint8pairtable.o gsnapl_sse2-splice-count.o gsnapl_sse2-support.o gsnapl_sse2-datadir.o gsnapl_sse2-parserange.o gsnapl_sse2-getline.o gsnapl_sse2-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes chmod +x md_coords chmod +x fa_coords chmod +x psl_splicesites chmod +x psl_introns chmod +x psl_genes chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_splicesites cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_introns chmod +x gtf_genes chmod +x gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x gff3_introns chmod +x gff3_genes chmod +x dbsnp_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' dh_auto_build --builddir build_ssse3 cd build_ssse3 && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.ssse3 gmap_ssse3-except.o gmap_ssse3-assert.o gmap_ssse3-mem.o gmap_ssse3-intlist.o gmap_ssse3-uintlist.o gmap_ssse3-list.o gmap_ssse3-littleendian.o gmap_ssse3-bigendian.o gmap_ssse3-univinterval.o gmap_ssse3-interval.o gmap_ssse3-stopwatch.o gmap_ssse3-semaphore.o gmap_ssse3-access.o gmap_ssse3-filestring.o gmap_ssse3-iit-read-univ.o gmap_ssse3-iit-read.o gmap_ssse3-md5.o gmap_ssse3-bzip2.o gmap_ssse3-fopen.o gmap_ssse3-sequence.o gmap_ssse3-reader.o gmap_ssse3-genomicpos.o gmap_ssse3-compress.o gmap_ssse3-compress-write.o gmap_ssse3-gbuffer.o gmap_ssse3-genome.o gmap_ssse3-popcount.o gmap_ssse3-dinucl_bits.o gmap_ssse3-genome_canonical.o gmap_ssse3-genome-write.o gmap_ssse3-bitpack64-read.o gmap_ssse3-bitpack64-readtwo.o gmap_ssse3-indexdb.o gmap_ssse3-oligo.o gmap_ssse3-block.o gmap_ssse3-chrom.o gmap_ssse3-segmentpos.o gmap_ssse3-chrnum.o gmap_ssse3-uinttable_rh.o gmap_ssse3-gregion.o gmap_ssse3-match.o gmap_ssse3-matchpool.o gmap_ssse3-diagnostic.o gmap_ssse3-stage1.o gmap_ssse3-diag.o gmap_ssse3-diagpool.o gmap_ssse3-cmet.o gmap_ssse3-atoi.o gmap_ssse3-orderstat.o gmap_ssse3-oligoindex_hr.o gmap_ssse3-intron.o gmap_ssse3-maxent.o gmap_ssse3-maxent_hr.o gmap_ssse3-pair.o gmap_ssse3-pairpool.o gmap_ssse3-cellpool.o gmap_ssse3-stage2.o gmap_ssse3-doublelist.o gmap_ssse3-smooth.o gmap_ssse3-splicestringpool.o gmap_ssse3-splicetrie_build.o gmap_ssse3-splicetrie.o gmap_ssse3-boyer-moore.o gmap_ssse3-dynprog.o gmap_ssse3-dynprog_simd.o gmap_ssse3-dynprog_single.o gmap_ssse3-dynprog_genome.o gmap_ssse3-dynprog_cdna.o gmap_ssse3-dynprog_end.o gmap_ssse3-translation.o gmap_ssse3-pbinom.o gmap_ssse3-changepoint.o gmap_ssse3-stage3.o gmap_ssse3-request.o gmap_ssse3-result.o gmap_ssse3-output.o gmap_ssse3-inbuffer.o gmap_ssse3-samheader.o gmap_ssse3-printbuffer.o gmap_ssse3-outbuffer.o gmap_ssse3-chimera.o gmap_ssse3-datadir.o gmap_ssse3-parserange.o gmap_ssse3-getline.o gmap_ssse3-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.ssse3 gsnap_ssse3-except.o gsnap_ssse3-assert.o gsnap_ssse3-mem.o gsnap_ssse3-intlist.o gsnap_ssse3-uintlist.o gsnap_ssse3-list.o gsnap_ssse3-littleendian.o gsnap_ssse3-bigendian.o gsnap_ssse3-univinterval.o gsnap_ssse3-interval.o gsnap_ssse3-stopwatch.o gsnap_ssse3-semaphore.o gsnap_ssse3-access.o gsnap_ssse3-filestring.o gsnap_ssse3-iit-read-univ.o gsnap_ssse3-iit-read.o gsnap_ssse3-bzip2.o gsnap_ssse3-reader.o gsnap_ssse3-genomicpos.o gsnap_ssse3-compress.o gsnap_ssse3-genome.o gsnap_ssse3-transcriptome.o gsnap_ssse3-popcount.o gsnap_ssse3-genomebits.o gsnap_ssse3-genomebits_consec.o gsnap_ssse3-genomebits_count.o gsnap_ssse3-genomebits_kmer.o gsnap_ssse3-genomebits_indel.o gsnap_ssse3-genomebits_decode.o gsnap_ssse3-genomebits_mismatches.o gsnap_ssse3-genomebits_trim.o gsnap_ssse3-dinucl_bits.o gsnap_ssse3-genome_sites.o gsnap_ssse3-bitpack64-read.o gsnap_ssse3-bitpack64-readtwo.o gsnap_ssse3-mergeinfo.o gsnap_ssse3-merge-diagonals-heap-uint4.o gsnap_ssse3-merge-uint4.o gsnap_ssse3-merge-diagonals-simd-uint4.o gsnap_ssse3-indexdb.o gsnap_ssse3-localdb-read.o gsnap_ssse3-oligo.o gsnap_ssse3-chrnum.o gsnap_ssse3-maxent_hr.o gsnap_ssse3-mapq.o gsnap_ssse3-fopen.o gsnap_ssse3-shortread.o gsnap_ssse3-junction.o gsnap_ssse3-concordance.o gsnap_ssse3-simplepair.o gsnap_ssse3-orderstat.o gsnap_ssse3-intlistpool.o gsnap_ssse3-uintlistpool.o gsnap_ssse3-listpool.o gsnap_ssse3-hitlistpool.o gsnap_ssse3-pathpool.o gsnap_ssse3-auxinfopool.o gsnap_ssse3-pathstorepool.o gsnap_ssse3-intron.o gsnap_ssse3-gbuffer.o gsnap_ssse3-select64-common.o gsnap_ssse3-select64-ones.o gsnap_ssse3-select64-zeroes.o gsnap_ssse3-ef64.o gsnap_ssse3-nr-x.o gsnap_ssse3-knownsplicing.o gsnap_ssse3-knownindels.o gsnap_ssse3-splice.o gsnap_ssse3-indel.o gsnap_ssse3-spliceendsgen.o gsnap_ssse3-spliceends.o gsnap_ssse3-bitpack64-access.o gsnap_ssse3-trdiag.o gsnap_ssse3-trdiagpool.o gsnap_ssse3-tr-extension-search.o gsnap_ssse3-univdiag.o gsnap_ssse3-univdiagpool.o gsnap_ssse3-sedgesort.o gsnap_ssse3-auxinfo.o gsnap_ssse3-pathstore.o gsnap_ssse3-altsplice.o gsnap_ssse3-path.o gsnap_ssse3-pathpair.o gsnap_ssse3-path-solve.o gsnap_ssse3-path-fusion.o gsnap_ssse3-path-trim.o gsnap_ssse3-path-eval.o gsnap_ssse3-pathpair-eval.o gsnap_ssse3-path-print-alignment.o gsnap_ssse3-path-print-m8.o gsnap_ssse3-path-print-sam.o gsnap_ssse3-path-learn.o gsnap_ssse3-method.o gsnap_ssse3-doublelist.o gsnap_ssse3-bitvector.o gsnap_ssse3-transcriptpool.o gsnap_ssse3-exon.o gsnap_ssse3-transcript.o gsnap_ssse3-trpathpool.o gsnap_ssse3-trpath.o gsnap_ssse3-trpath-solve.o gsnap_ssse3-trpath-convert.o gsnap_ssse3-trpath-eval.o gsnap_ssse3-transcriptome-search.o gsnap_ssse3-vectorpool.o gsnap_ssse3-repair.o gsnap_ssse3-transcript-remap.o gsnap_ssse3-transcript-velocity.o gsnap_ssse3-intersect-small.o gsnap_ssse3-intersect-uint2.o gsnap_ssse3-intersect-approx-uint4.o gsnap_ssse3-intersect-approx-indices-uint4.o gsnap_ssse3-intersect-wdups-indices.o gsnap_ssse3-intersect-lower-small.o gsnap_ssse3-intersect-higher-small.o gsnap_ssse3-intersect-indices-small.o gsnap_ssse3-intersect-indices2-small.o gsnap_ssse3-intersect-concordance-uint4.o gsnap_ssse3-kmer-search.o gsnap_ssse3-extension-search.o gsnap_ssse3-repetitive.o gsnap_ssse3-uint8table.o gsnap_ssse3-uinttable.o gsnap_ssse3-stage1hr.o gsnap_ssse3-stage1hr-single.o gsnap_ssse3-stage1hr-paired.o gsnap_ssse3-uinttableuint.o gsnap_ssse3-tableuint.o gsnap_ssse3-single-cell.o gsnap_ssse3-request.o gsnap_ssse3-resulthr.o gsnap_ssse3-output.o gsnap_ssse3-inbuffer.o gsnap_ssse3-samheader.o gsnap_ssse3-printbuffer.o gsnap_ssse3-outbuffer.o gsnap_ssse3-uintpairtable.o gsnap_ssse3-splice-count.o gsnap_ssse3-support.o gsnap_ssse3-datadir.o gsnap_ssse3-parserange.o gsnap_ssse3-getline.o gsnap_ssse3-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.ssse3 gmapl_ssse3-except.o gmapl_ssse3-assert.o gmapl_ssse3-mem.o gmapl_ssse3-intlist.o gmapl_ssse3-uintlist.o gmapl_ssse3-uint8list.o gmapl_ssse3-list.o gmapl_ssse3-littleendian.o gmapl_ssse3-bigendian.o gmapl_ssse3-univinterval.o gmapl_ssse3-interval.o gmapl_ssse3-stopwatch.o gmapl_ssse3-semaphore.o gmapl_ssse3-access.o gmapl_ssse3-filestring.o gmapl_ssse3-iit-read-univ.o gmapl_ssse3-iit-read.o gmapl_ssse3-md5.o gmapl_ssse3-bzip2.o gmapl_ssse3-fopen.o gmapl_ssse3-sequence.o gmapl_ssse3-reader.o gmapl_ssse3-genomicpos.o gmapl_ssse3-compress.o gmapl_ssse3-compress-write.o gmapl_ssse3-gbuffer.o gmapl_ssse3-genome.o gmapl_ssse3-popcount.o gmapl_ssse3-dinucl_bits.o gmapl_ssse3-genome_canonical.o gmapl_ssse3-genome-write.o gmapl_ssse3-bitpack64-read.o gmapl_ssse3-bitpack64-readtwo.o gmapl_ssse3-indexdb.o gmapl_ssse3-oligo.o gmapl_ssse3-block.o gmapl_ssse3-chrom.o gmapl_ssse3-segmentpos.o gmapl_ssse3-chrnum.o gmapl_ssse3-uinttable_rh.o gmapl_ssse3-uint8table_rh.o gmapl_ssse3-gregion.o gmapl_ssse3-match.o gmapl_ssse3-matchpool.o gmapl_ssse3-diagnostic.o gmapl_ssse3-stage1.o gmapl_ssse3-diag.o gmapl_ssse3-diagpool.o gmapl_ssse3-cmet.o gmapl_ssse3-atoi.o gmapl_ssse3-orderstat.o gmapl_ssse3-oligoindex_hr.o gmapl_ssse3-intron.o gmapl_ssse3-maxent.o gmapl_ssse3-maxent_hr.o gmapl_ssse3-pair.o gmapl_ssse3-pairpool.o gmapl_ssse3-cellpool.o gmapl_ssse3-stage2.o gmapl_ssse3-doublelist.o gmapl_ssse3-smooth.o gmapl_ssse3-splicestringpool.o gmapl_ssse3-splicetrie_build.o gmapl_ssse3-splicetrie.o gmapl_ssse3-boyer-moore.o gmapl_ssse3-dynprog.o gmapl_ssse3-dynprog_simd.o gmapl_ssse3-dynprog_single.o gmapl_ssse3-dynprog_genome.o gmapl_ssse3-dynprog_cdna.o gmapl_ssse3-dynprog_end.o gmapl_ssse3-translation.o gmapl_ssse3-pbinom.o gmapl_ssse3-changepoint.o gmapl_ssse3-stage3.o gmapl_ssse3-request.o gmapl_ssse3-result.o gmapl_ssse3-output.o gmapl_ssse3-inbuffer.o gmapl_ssse3-samheader.o gmapl_ssse3-printbuffer.o gmapl_ssse3-outbuffer.o gmapl_ssse3-chimera.o gmapl_ssse3-datadir.o gmapl_ssse3-parserange.o gmapl_ssse3-getline.o gmapl_ssse3-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.ssse3 gsnapl_ssse3-except.o gsnapl_ssse3-assert.o gsnapl_ssse3-mem.o gsnapl_ssse3-intlist.o gsnapl_ssse3-uintlist.o gsnapl_ssse3-uint8list.o gsnapl_ssse3-list.o gsnapl_ssse3-littleendian.o gsnapl_ssse3-bigendian.o gsnapl_ssse3-univinterval.o gsnapl_ssse3-interval.o gsnapl_ssse3-stopwatch.o gsnapl_ssse3-semaphore.o gsnapl_ssse3-access.o gsnapl_ssse3-filestring.o gsnapl_ssse3-iit-read-univ.o gsnapl_ssse3-iit-read.o gsnapl_ssse3-bzip2.o gsnapl_ssse3-reader.o gsnapl_ssse3-genomicpos.o gsnapl_ssse3-compress.o gsnapl_ssse3-genome.o gsnapl_ssse3-transcriptome.o gsnapl_ssse3-popcount.o gsnapl_ssse3-genomebits.o gsnapl_ssse3-genomebits_consec.o gsnapl_ssse3-genomebits_count.o gsnapl_ssse3-genomebits_kmer.o gsnapl_ssse3-genomebits_indel.o gsnapl_ssse3-genomebits_decode.o gsnapl_ssse3-genomebits_mismatches.o gsnapl_ssse3-genomebits_trim.o gsnapl_ssse3-dinucl_bits.o gsnapl_ssse3-genome_sites.o gsnapl_ssse3-bitpack64-read.o gsnapl_ssse3-bitpack64-readtwo.o gsnapl_ssse3-mergeinfo.o gsnapl_ssse3-merge-diagonals-heap-uint8.o gsnapl_ssse3-merge-uint8.o gsnapl_ssse3-merge-diagonals-simd-uint8.o gsnapl_ssse3-merge-diagonals-heap-uint4.o gsnapl_ssse3-merge-uint4.o gsnapl_ssse3-merge-diagonals-simd-uint4.o gsnapl_ssse3-indexdb.o gsnapl_ssse3-localdb-read.o gsnapl_ssse3-oligo.o gsnapl_ssse3-chrnum.o gsnapl_ssse3-maxent_hr.o gsnapl_ssse3-mapq.o gsnapl_ssse3-fopen.o gsnapl_ssse3-shortread.o gsnapl_ssse3-junction.o gsnapl_ssse3-concordance.o gsnapl_ssse3-simplepair.o gsnapl_ssse3-orderstat.o gsnapl_ssse3-intlistpool.o gsnapl_ssse3-uintlistpool.o gsnapl_ssse3-uint8listpool.o gsnapl_ssse3-listpool.o gsnapl_ssse3-hitlistpool.o gsnapl_ssse3-pathpool.o gsnapl_ssse3-auxinfopool.o gsnapl_ssse3-pathstorepool.o gsnapl_ssse3-intron.o gsnapl_ssse3-gbuffer.o gsnapl_ssse3-select64-common.o gsnapl_ssse3-select64-ones.o gsnapl_ssse3-select64-zeroes.o gsnapl_ssse3-ef64.o gsnapl_ssse3-nr-x.o gsnapl_ssse3-knownsplicing.o gsnapl_ssse3-knownindels.o gsnapl_ssse3-splice.o gsnapl_ssse3-indel.o gsnapl_ssse3-spliceendsgen.o gsnapl_ssse3-spliceends.o gsnapl_ssse3-bitpack64-access.o gsnapl_ssse3-trdiag.o gsnapl_ssse3-trdiagpool.o gsnapl_ssse3-tr-extension-search.o gsnapl_ssse3-univdiag.o gsnapl_ssse3-univdiagpool.o gsnapl_ssse3-sedgesort.o gsnapl_ssse3-auxinfo.o gsnapl_ssse3-pathstore.o gsnapl_ssse3-altsplice.o gsnapl_ssse3-path.o gsnapl_ssse3-pathpair.o gsnapl_ssse3-path-solve.o gsnapl_ssse3-path-fusion.o gsnapl_ssse3-path-trim.o gsnapl_ssse3-path-eval.o gsnapl_ssse3-pathpair-eval.o gsnapl_ssse3-path-print-alignment.o gsnapl_ssse3-path-print-m8.o gsnapl_ssse3-path-print-sam.o gsnapl_ssse3-path-learn.o gsnapl_ssse3-method.o gsnapl_ssse3-doublelist.o gsnapl_ssse3-bitvector.o gsnapl_ssse3-transcriptpool.o gsnapl_ssse3-exon.o gsnapl_ssse3-transcript.o gsnapl_ssse3-trpathpool.o gsnapl_ssse3-trpath.o gsnapl_ssse3-trpath-solve.o gsnapl_ssse3-trpath-convert.o gsnapl_ssse3-trpath-eval.o gsnapl_ssse3-transcriptome-search.o gsnapl_ssse3-vectorpool.o gsnapl_ssse3-repair.o gsnapl_ssse3-transcript-remap.o gsnapl_ssse3-transcript-velocity.o gsnapl_ssse3-intersect-large.o gsnapl_ssse3-intersect-small.o gsnapl_ssse3-intersect-uint2.o gsnapl_ssse3-intersect-approx-uint4.o gsnapl_ssse3-intersect-approx-uint8.o gsnapl_ssse3-intersect-approx-indices-uint8.o gsnapl_ssse3-intersect-wdups-indices.o gsnapl_ssse3-intersect-lower-large.o gsnapl_ssse3-intersect-higher-large.o gsnapl_ssse3-intersect-indices-small.o gsnapl_ssse3-intersect-indices2-large.o gsnapl_ssse3-intersect-indices-uint8.o gsnapl_ssse3-intersect-concordance-uint8.o gsnapl_ssse3-kmer-search.o gsnapl_ssse3-extension-search.o gsnapl_ssse3-repetitive.o gsnapl_ssse3-uint8table.o gsnapl_ssse3-stage1hr.o gsnapl_ssse3-stage1hr-single.o gsnapl_ssse3-stage1hr-paired.o gsnapl_ssse3-uint8tableuint.o gsnapl_ssse3-tableuint.o gsnapl_ssse3-single-cell.o gsnapl_ssse3-request.o gsnapl_ssse3-resulthr.o gsnapl_ssse3-output.o gsnapl_ssse3-inbuffer.o gsnapl_ssse3-samheader.o gsnapl_ssse3-printbuffer.o gsnapl_ssse3-outbuffer.o gsnapl_ssse3-uint8pairtable.o gsnapl_ssse3-splice-count.o gsnapl_ssse3-support.o gsnapl_ssse3-datadir.o gsnapl_ssse3-parserange.o gsnapl_ssse3-getline.o gsnapl_ssse3-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns chmod +x fa_coords chmod +x md_coords chmod +x psl_splicesites chmod +x psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x psl_genes cp gtf_genes.pl gtf_genes chmod +x ensembl_genes chmod +x gtf_splicesites chmod +x gtf_introns cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes chmod +x gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_introns chmod +x gff3_genes chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' dh_auto_build --builddir build_sse41 cd build_sse41 && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read.c: In function 'IIT_read': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c: In function 'IIT_read': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse41 gmapl_sse41-except.o gmapl_sse41-assert.o gmapl_sse41-mem.o gmapl_sse41-intlist.o gmapl_sse41-uintlist.o gmapl_sse41-uint8list.o gmapl_sse41-list.o gmapl_sse41-littleendian.o gmapl_sse41-bigendian.o gmapl_sse41-univinterval.o gmapl_sse41-interval.o gmapl_sse41-stopwatch.o gmapl_sse41-semaphore.o gmapl_sse41-access.o gmapl_sse41-filestring.o gmapl_sse41-iit-read-univ.o gmapl_sse41-iit-read.o gmapl_sse41-md5.o gmapl_sse41-bzip2.o gmapl_sse41-fopen.o gmapl_sse41-sequence.o gmapl_sse41-reader.o gmapl_sse41-genomicpos.o gmapl_sse41-compress.o gmapl_sse41-compress-write.o gmapl_sse41-gbuffer.o gmapl_sse41-genome.o gmapl_sse41-popcount.o gmapl_sse41-dinucl_bits.o gmapl_sse41-genome_canonical.o gmapl_sse41-genome-write.o gmapl_sse41-bitpack64-read.o gmapl_sse41-bitpack64-readtwo.o gmapl_sse41-indexdb.o gmapl_sse41-oligo.o gmapl_sse41-block.o gmapl_sse41-chrom.o gmapl_sse41-segmentpos.o gmapl_sse41-chrnum.o gmapl_sse41-uinttable_rh.o gmapl_sse41-uint8table_rh.o gmapl_sse41-gregion.o gmapl_sse41-match.o gmapl_sse41-matchpool.o gmapl_sse41-diagnostic.o gmapl_sse41-stage1.o gmapl_sse41-diag.o gmapl_sse41-diagpool.o gmapl_sse41-cmet.o gmapl_sse41-atoi.o gmapl_sse41-orderstat.o gmapl_sse41-oligoindex_hr.o gmapl_sse41-intron.o gmapl_sse41-maxent.o gmapl_sse41-maxent_hr.o gmapl_sse41-pair.o gmapl_sse41-pairpool.o gmapl_sse41-cellpool.o gmapl_sse41-stage2.o gmapl_sse41-doublelist.o gmapl_sse41-smooth.o gmapl_sse41-splicestringpool.o gmapl_sse41-splicetrie_build.o gmapl_sse41-splicetrie.o gmapl_sse41-boyer-moore.o gmapl_sse41-dynprog.o gmapl_sse41-dynprog_simd.o gmapl_sse41-dynprog_single.o gmapl_sse41-dynprog_genome.o gmapl_sse41-dynprog_cdna.o gmapl_sse41-dynprog_end.o gmapl_sse41-translation.o gmapl_sse41-pbinom.o gmapl_sse41-changepoint.o gmapl_sse41-stage3.o gmapl_sse41-request.o gmapl_sse41-result.o gmapl_sse41-output.o gmapl_sse41-inbuffer.o gmapl_sse41-samheader.o gmapl_sse41-printbuffer.o gmapl_sse41-outbuffer.o gmapl_sse41-chimera.o gmapl_sse41-datadir.o gmapl_sse41-parserange.o gmapl_sse41-getline.o gmapl_sse41-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse41 gmap_sse41-except.o gmap_sse41-assert.o gmap_sse41-mem.o gmap_sse41-intlist.o gmap_sse41-uintlist.o gmap_sse41-list.o gmap_sse41-littleendian.o gmap_sse41-bigendian.o gmap_sse41-univinterval.o gmap_sse41-interval.o gmap_sse41-stopwatch.o gmap_sse41-semaphore.o gmap_sse41-access.o gmap_sse41-filestring.o gmap_sse41-iit-read-univ.o gmap_sse41-iit-read.o gmap_sse41-md5.o gmap_sse41-bzip2.o gmap_sse41-fopen.o gmap_sse41-sequence.o gmap_sse41-reader.o gmap_sse41-genomicpos.o gmap_sse41-compress.o gmap_sse41-compress-write.o gmap_sse41-gbuffer.o gmap_sse41-genome.o gmap_sse41-popcount.o gmap_sse41-dinucl_bits.o gmap_sse41-genome_canonical.o gmap_sse41-genome-write.o gmap_sse41-bitpack64-read.o gmap_sse41-bitpack64-readtwo.o gmap_sse41-indexdb.o gmap_sse41-oligo.o gmap_sse41-block.o gmap_sse41-chrom.o gmap_sse41-segmentpos.o gmap_sse41-chrnum.o gmap_sse41-uinttable_rh.o gmap_sse41-gregion.o gmap_sse41-match.o gmap_sse41-matchpool.o gmap_sse41-diagnostic.o gmap_sse41-stage1.o gmap_sse41-diag.o gmap_sse41-diagpool.o gmap_sse41-cmet.o gmap_sse41-atoi.o gmap_sse41-orderstat.o gmap_sse41-oligoindex_hr.o gmap_sse41-intron.o gmap_sse41-maxent.o gmap_sse41-maxent_hr.o gmap_sse41-pair.o gmap_sse41-pairpool.o gmap_sse41-cellpool.o gmap_sse41-stage2.o gmap_sse41-doublelist.o gmap_sse41-smooth.o gmap_sse41-splicestringpool.o gmap_sse41-splicetrie_build.o gmap_sse41-splicetrie.o gmap_sse41-boyer-moore.o gmap_sse41-dynprog.o gmap_sse41-dynprog_simd.o gmap_sse41-dynprog_single.o gmap_sse41-dynprog_genome.o gmap_sse41-dynprog_cdna.o gmap_sse41-dynprog_end.o gmap_sse41-translation.o gmap_sse41-pbinom.o gmap_sse41-changepoint.o gmap_sse41-stage3.o gmap_sse41-request.o gmap_sse41-result.o gmap_sse41-output.o gmap_sse41-inbuffer.o gmap_sse41-samheader.o gmap_sse41-printbuffer.o gmap_sse41-outbuffer.o gmap_sse41-chimera.o gmap_sse41-datadir.o gmap_sse41-parserange.o gmap_sse41-getline.o gmap_sse41-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse41 gsnap_sse41-except.o gsnap_sse41-assert.o gsnap_sse41-mem.o gsnap_sse41-intlist.o gsnap_sse41-uintlist.o gsnap_sse41-list.o gsnap_sse41-littleendian.o gsnap_sse41-bigendian.o gsnap_sse41-univinterval.o gsnap_sse41-interval.o gsnap_sse41-stopwatch.o gsnap_sse41-semaphore.o gsnap_sse41-access.o gsnap_sse41-filestring.o gsnap_sse41-iit-read-univ.o gsnap_sse41-iit-read.o gsnap_sse41-bzip2.o gsnap_sse41-reader.o gsnap_sse41-genomicpos.o gsnap_sse41-compress.o gsnap_sse41-genome.o gsnap_sse41-transcriptome.o gsnap_sse41-popcount.o gsnap_sse41-genomebits.o gsnap_sse41-genomebits_consec.o gsnap_sse41-genomebits_count.o gsnap_sse41-genomebits_kmer.o gsnap_sse41-genomebits_indel.o gsnap_sse41-genomebits_decode.o gsnap_sse41-genomebits_mismatches.o gsnap_sse41-genomebits_trim.o gsnap_sse41-dinucl_bits.o gsnap_sse41-genome_sites.o gsnap_sse41-bitpack64-read.o gsnap_sse41-bitpack64-readtwo.o gsnap_sse41-mergeinfo.o gsnap_sse41-merge-diagonals-heap-uint4.o gsnap_sse41-merge-uint4.o gsnap_sse41-merge-diagonals-simd-uint4.o gsnap_sse41-indexdb.o gsnap_sse41-localdb-read.o gsnap_sse41-oligo.o gsnap_sse41-chrnum.o gsnap_sse41-maxent_hr.o gsnap_sse41-mapq.o gsnap_sse41-fopen.o gsnap_sse41-shortread.o gsnap_sse41-junction.o gsnap_sse41-concordance.o gsnap_sse41-simplepair.o gsnap_sse41-orderstat.o gsnap_sse41-intlistpool.o gsnap_sse41-uintlistpool.o gsnap_sse41-listpool.o gsnap_sse41-hitlistpool.o gsnap_sse41-pathpool.o gsnap_sse41-auxinfopool.o gsnap_sse41-pathstorepool.o gsnap_sse41-intron.o gsnap_sse41-gbuffer.o gsnap_sse41-select64-common.o gsnap_sse41-select64-ones.o gsnap_sse41-select64-zeroes.o gsnap_sse41-ef64.o gsnap_sse41-nr-x.o gsnap_sse41-knownsplicing.o gsnap_sse41-knownindels.o gsnap_sse41-splice.o gsnap_sse41-indel.o gsnap_sse41-spliceendsgen.o gsnap_sse41-spliceends.o gsnap_sse41-bitpack64-access.o gsnap_sse41-trdiag.o gsnap_sse41-trdiagpool.o gsnap_sse41-tr-extension-search.o gsnap_sse41-univdiag.o gsnap_sse41-univdiagpool.o gsnap_sse41-sedgesort.o gsnap_sse41-auxinfo.o gsnap_sse41-pathstore.o gsnap_sse41-altsplice.o gsnap_sse41-path.o gsnap_sse41-pathpair.o gsnap_sse41-path-solve.o gsnap_sse41-path-fusion.o gsnap_sse41-path-trim.o gsnap_sse41-path-eval.o gsnap_sse41-pathpair-eval.o gsnap_sse41-path-print-alignment.o gsnap_sse41-path-print-m8.o gsnap_sse41-path-print-sam.o gsnap_sse41-path-learn.o gsnap_sse41-method.o gsnap_sse41-doublelist.o gsnap_sse41-bitvector.o gsnap_sse41-transcriptpool.o gsnap_sse41-exon.o gsnap_sse41-transcript.o gsnap_sse41-trpathpool.o gsnap_sse41-trpath.o gsnap_sse41-trpath-solve.o gsnap_sse41-trpath-convert.o gsnap_sse41-trpath-eval.o gsnap_sse41-transcriptome-search.o gsnap_sse41-vectorpool.o gsnap_sse41-repair.o gsnap_sse41-transcript-remap.o gsnap_sse41-transcript-velocity.o gsnap_sse41-intersect-small.o gsnap_sse41-intersect-uint2.o gsnap_sse41-intersect-approx-uint4.o gsnap_sse41-intersect-approx-indices-uint4.o gsnap_sse41-intersect-wdups-indices.o gsnap_sse41-intersect-lower-small.o gsnap_sse41-intersect-higher-small.o gsnap_sse41-intersect-indices-small.o gsnap_sse41-intersect-indices2-small.o gsnap_sse41-intersect-concordance-uint4.o gsnap_sse41-kmer-search.o gsnap_sse41-extension-search.o gsnap_sse41-repetitive.o gsnap_sse41-uint8table.o gsnap_sse41-uinttable.o gsnap_sse41-stage1hr.o gsnap_sse41-stage1hr-single.o gsnap_sse41-stage1hr-paired.o gsnap_sse41-uinttableuint.o gsnap_sse41-tableuint.o gsnap_sse41-single-cell.o gsnap_sse41-request.o gsnap_sse41-resulthr.o gsnap_sse41-output.o gsnap_sse41-inbuffer.o gsnap_sse41-samheader.o gsnap_sse41-printbuffer.o gsnap_sse41-outbuffer.o gsnap_sse41-uintpairtable.o gsnap_sse41-splice-count.o gsnap_sse41-support.o gsnap_sse41-datadir.o gsnap_sse41-parserange.o gsnap_sse41-getline.o gsnap_sse41-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse41 gsnapl_sse41-except.o gsnapl_sse41-assert.o gsnapl_sse41-mem.o gsnapl_sse41-intlist.o gsnapl_sse41-uintlist.o gsnapl_sse41-uint8list.o gsnapl_sse41-list.o gsnapl_sse41-littleendian.o gsnapl_sse41-bigendian.o gsnapl_sse41-univinterval.o gsnapl_sse41-interval.o gsnapl_sse41-stopwatch.o gsnapl_sse41-semaphore.o gsnapl_sse41-access.o gsnapl_sse41-filestring.o gsnapl_sse41-iit-read-univ.o gsnapl_sse41-iit-read.o gsnapl_sse41-bzip2.o gsnapl_sse41-reader.o gsnapl_sse41-genomicpos.o gsnapl_sse41-compress.o gsnapl_sse41-genome.o gsnapl_sse41-transcriptome.o gsnapl_sse41-popcount.o gsnapl_sse41-genomebits.o gsnapl_sse41-genomebits_consec.o gsnapl_sse41-genomebits_count.o gsnapl_sse41-genomebits_kmer.o gsnapl_sse41-genomebits_indel.o gsnapl_sse41-genomebits_decode.o gsnapl_sse41-genomebits_mismatches.o gsnapl_sse41-genomebits_trim.o gsnapl_sse41-dinucl_bits.o gsnapl_sse41-genome_sites.o gsnapl_sse41-bitpack64-read.o gsnapl_sse41-bitpack64-readtwo.o gsnapl_sse41-mergeinfo.o gsnapl_sse41-merge-diagonals-heap-uint8.o gsnapl_sse41-merge-uint8.o gsnapl_sse41-merge-diagonals-simd-uint8.o gsnapl_sse41-merge-diagonals-heap-uint4.o gsnapl_sse41-merge-uint4.o gsnapl_sse41-merge-diagonals-simd-uint4.o gsnapl_sse41-indexdb.o gsnapl_sse41-localdb-read.o gsnapl_sse41-oligo.o gsnapl_sse41-chrnum.o gsnapl_sse41-maxent_hr.o gsnapl_sse41-mapq.o gsnapl_sse41-fopen.o gsnapl_sse41-shortread.o gsnapl_sse41-junction.o gsnapl_sse41-concordance.o gsnapl_sse41-simplepair.o gsnapl_sse41-orderstat.o gsnapl_sse41-intlistpool.o gsnapl_sse41-uintlistpool.o gsnapl_sse41-uint8listpool.o gsnapl_sse41-listpool.o gsnapl_sse41-hitlistpool.o gsnapl_sse41-pathpool.o gsnapl_sse41-auxinfopool.o gsnapl_sse41-pathstorepool.o gsnapl_sse41-intron.o gsnapl_sse41-gbuffer.o gsnapl_sse41-select64-common.o gsnapl_sse41-select64-ones.o gsnapl_sse41-select64-zeroes.o gsnapl_sse41-ef64.o gsnapl_sse41-nr-x.o gsnapl_sse41-knownsplicing.o gsnapl_sse41-knownindels.o gsnapl_sse41-splice.o gsnapl_sse41-indel.o gsnapl_sse41-spliceendsgen.o gsnapl_sse41-spliceends.o gsnapl_sse41-bitpack64-access.o gsnapl_sse41-trdiag.o gsnapl_sse41-trdiagpool.o gsnapl_sse41-tr-extension-search.o gsnapl_sse41-univdiag.o gsnapl_sse41-univdiagpool.o gsnapl_sse41-sedgesort.o gsnapl_sse41-auxinfo.o gsnapl_sse41-pathstore.o gsnapl_sse41-altsplice.o gsnapl_sse41-path.o gsnapl_sse41-pathpair.o gsnapl_sse41-path-solve.o gsnapl_sse41-path-fusion.o gsnapl_sse41-path-trim.o gsnapl_sse41-path-eval.o gsnapl_sse41-pathpair-eval.o gsnapl_sse41-path-print-alignment.o gsnapl_sse41-path-print-m8.o gsnapl_sse41-path-print-sam.o gsnapl_sse41-path-learn.o gsnapl_sse41-method.o gsnapl_sse41-doublelist.o gsnapl_sse41-bitvector.o gsnapl_sse41-transcriptpool.o gsnapl_sse41-exon.o gsnapl_sse41-transcript.o gsnapl_sse41-trpathpool.o gsnapl_sse41-trpath.o gsnapl_sse41-trpath-solve.o gsnapl_sse41-trpath-convert.o gsnapl_sse41-trpath-eval.o gsnapl_sse41-transcriptome-search.o gsnapl_sse41-vectorpool.o gsnapl_sse41-repair.o gsnapl_sse41-transcript-remap.o gsnapl_sse41-transcript-velocity.o gsnapl_sse41-intersect-large.o gsnapl_sse41-intersect-small.o gsnapl_sse41-intersect-uint2.o gsnapl_sse41-intersect-approx-uint4.o gsnapl_sse41-intersect-approx-uint8.o gsnapl_sse41-intersect-approx-indices-uint8.o gsnapl_sse41-intersect-wdups-indices.o gsnapl_sse41-intersect-lower-large.o gsnapl_sse41-intersect-higher-large.o gsnapl_sse41-intersect-indices-small.o gsnapl_sse41-intersect-indices2-large.o gsnapl_sse41-intersect-indices-uint8.o gsnapl_sse41-intersect-concordance-uint8.o gsnapl_sse41-kmer-search.o gsnapl_sse41-extension-search.o gsnapl_sse41-repetitive.o gsnapl_sse41-uint8table.o gsnapl_sse41-stage1hr.o gsnapl_sse41-stage1hr-single.o gsnapl_sse41-stage1hr-paired.o gsnapl_sse41-uint8tableuint.o gsnapl_sse41-tableuint.o gsnapl_sse41-single-cell.o gsnapl_sse41-request.o gsnapl_sse41-resulthr.o gsnapl_sse41-output.o gsnapl_sse41-inbuffer.o gsnapl_sse41-samheader.o gsnapl_sse41-printbuffer.o gsnapl_sse41-outbuffer.o gsnapl_sse41-uint8pairtable.o gsnapl_sse41-splice-count.o gsnapl_sse41-support.o gsnapl_sse41-datadir.o gsnapl_sse41-parserange.o gsnapl_sse41-getline.o gsnapl_sse41-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites chmod +x fa_coords chmod +x psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gtf_genes chmod +x psl_introns chmod +x psl_genes chmod +x ensembl_genes chmod +x gtf_splicesites chmod +x gtf_introns chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites chmod +x gff3_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x gff3_genes chmod +x dbsnp_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' dh_auto_build --builddir build_sse42 cd build_sse42 && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c ../../src/indexdb.c: In function 'positions_read_multiple_large': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse42 gmap_sse42-except.o gmap_sse42-assert.o gmap_sse42-mem.o gmap_sse42-intlist.o gmap_sse42-uintlist.o gmap_sse42-list.o gmap_sse42-littleendian.o gmap_sse42-bigendian.o gmap_sse42-univinterval.o gmap_sse42-interval.o gmap_sse42-stopwatch.o gmap_sse42-semaphore.o gmap_sse42-access.o gmap_sse42-filestring.o gmap_sse42-iit-read-univ.o gmap_sse42-iit-read.o gmap_sse42-md5.o gmap_sse42-bzip2.o gmap_sse42-fopen.o gmap_sse42-sequence.o gmap_sse42-reader.o gmap_sse42-genomicpos.o gmap_sse42-compress.o gmap_sse42-compress-write.o gmap_sse42-gbuffer.o gmap_sse42-genome.o gmap_sse42-popcount.o gmap_sse42-dinucl_bits.o gmap_sse42-genome_canonical.o gmap_sse42-genome-write.o gmap_sse42-bitpack64-read.o gmap_sse42-bitpack64-readtwo.o gmap_sse42-indexdb.o gmap_sse42-oligo.o gmap_sse42-block.o gmap_sse42-chrom.o gmap_sse42-segmentpos.o gmap_sse42-chrnum.o gmap_sse42-uinttable_rh.o gmap_sse42-gregion.o gmap_sse42-match.o gmap_sse42-matchpool.o gmap_sse42-diagnostic.o gmap_sse42-stage1.o gmap_sse42-diag.o gmap_sse42-diagpool.o gmap_sse42-cmet.o gmap_sse42-atoi.o gmap_sse42-orderstat.o gmap_sse42-oligoindex_hr.o gmap_sse42-intron.o gmap_sse42-maxent.o gmap_sse42-maxent_hr.o gmap_sse42-pair.o gmap_sse42-pairpool.o gmap_sse42-cellpool.o gmap_sse42-stage2.o gmap_sse42-doublelist.o gmap_sse42-smooth.o gmap_sse42-splicestringpool.o gmap_sse42-splicetrie_build.o gmap_sse42-splicetrie.o gmap_sse42-boyer-moore.o gmap_sse42-dynprog.o gmap_sse42-dynprog_simd.o gmap_sse42-dynprog_single.o gmap_sse42-dynprog_genome.o gmap_sse42-dynprog_cdna.o gmap_sse42-dynprog_end.o gmap_sse42-translation.o gmap_sse42-pbinom.o gmap_sse42-changepoint.o gmap_sse42-stage3.o gmap_sse42-request.o gmap_sse42-result.o gmap_sse42-output.o gmap_sse42-inbuffer.o gmap_sse42-samheader.o gmap_sse42-printbuffer.o gmap_sse42-outbuffer.o gmap_sse42-chimera.o gmap_sse42-datadir.o gmap_sse42-parserange.o gmap_sse42-getline.o gmap_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse42 gmapl_sse42-except.o gmapl_sse42-assert.o gmapl_sse42-mem.o gmapl_sse42-intlist.o gmapl_sse42-uintlist.o gmapl_sse42-uint8list.o gmapl_sse42-list.o gmapl_sse42-littleendian.o gmapl_sse42-bigendian.o gmapl_sse42-univinterval.o gmapl_sse42-interval.o gmapl_sse42-stopwatch.o gmapl_sse42-semaphore.o gmapl_sse42-access.o gmapl_sse42-filestring.o gmapl_sse42-iit-read-univ.o gmapl_sse42-iit-read.o gmapl_sse42-md5.o gmapl_sse42-bzip2.o gmapl_sse42-fopen.o gmapl_sse42-sequence.o gmapl_sse42-reader.o gmapl_sse42-genomicpos.o gmapl_sse42-compress.o gmapl_sse42-compress-write.o gmapl_sse42-gbuffer.o gmapl_sse42-genome.o gmapl_sse42-popcount.o gmapl_sse42-dinucl_bits.o gmapl_sse42-genome_canonical.o gmapl_sse42-genome-write.o gmapl_sse42-bitpack64-read.o gmapl_sse42-bitpack64-readtwo.o gmapl_sse42-indexdb.o gmapl_sse42-oligo.o gmapl_sse42-block.o gmapl_sse42-chrom.o gmapl_sse42-segmentpos.o gmapl_sse42-chrnum.o gmapl_sse42-uinttable_rh.o gmapl_sse42-uint8table_rh.o gmapl_sse42-gregion.o gmapl_sse42-match.o gmapl_sse42-matchpool.o gmapl_sse42-diagnostic.o gmapl_sse42-stage1.o gmapl_sse42-diag.o gmapl_sse42-diagpool.o gmapl_sse42-cmet.o gmapl_sse42-atoi.o gmapl_sse42-orderstat.o gmapl_sse42-oligoindex_hr.o gmapl_sse42-intron.o gmapl_sse42-maxent.o gmapl_sse42-maxent_hr.o gmapl_sse42-pair.o gmapl_sse42-pairpool.o gmapl_sse42-cellpool.o gmapl_sse42-stage2.o gmapl_sse42-doublelist.o gmapl_sse42-smooth.o gmapl_sse42-splicestringpool.o gmapl_sse42-splicetrie_build.o gmapl_sse42-splicetrie.o gmapl_sse42-boyer-moore.o gmapl_sse42-dynprog.o gmapl_sse42-dynprog_simd.o gmapl_sse42-dynprog_single.o gmapl_sse42-dynprog_genome.o gmapl_sse42-dynprog_cdna.o gmapl_sse42-dynprog_end.o gmapl_sse42-translation.o gmapl_sse42-pbinom.o gmapl_sse42-changepoint.o gmapl_sse42-stage3.o gmapl_sse42-request.o gmapl_sse42-result.o gmapl_sse42-output.o gmapl_sse42-inbuffer.o gmapl_sse42-samheader.o gmapl_sse42-printbuffer.o gmapl_sse42-outbuffer.o gmapl_sse42-chimera.o gmapl_sse42-datadir.o gmapl_sse42-parserange.o gmapl_sse42-getline.o gmapl_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse42 gsnap_sse42-except.o gsnap_sse42-assert.o gsnap_sse42-mem.o gsnap_sse42-intlist.o gsnap_sse42-uintlist.o gsnap_sse42-list.o gsnap_sse42-littleendian.o gsnap_sse42-bigendian.o gsnap_sse42-univinterval.o gsnap_sse42-interval.o gsnap_sse42-stopwatch.o gsnap_sse42-semaphore.o gsnap_sse42-access.o gsnap_sse42-filestring.o gsnap_sse42-iit-read-univ.o gsnap_sse42-iit-read.o gsnap_sse42-bzip2.o gsnap_sse42-reader.o gsnap_sse42-genomicpos.o gsnap_sse42-compress.o gsnap_sse42-genome.o gsnap_sse42-transcriptome.o gsnap_sse42-popcount.o gsnap_sse42-genomebits.o gsnap_sse42-genomebits_consec.o gsnap_sse42-genomebits_count.o gsnap_sse42-genomebits_kmer.o gsnap_sse42-genomebits_indel.o gsnap_sse42-genomebits_decode.o gsnap_sse42-genomebits_mismatches.o gsnap_sse42-genomebits_trim.o gsnap_sse42-dinucl_bits.o gsnap_sse42-genome_sites.o gsnap_sse42-bitpack64-read.o gsnap_sse42-bitpack64-readtwo.o gsnap_sse42-mergeinfo.o gsnap_sse42-merge-diagonals-heap-uint4.o gsnap_sse42-merge-uint4.o gsnap_sse42-merge-diagonals-simd-uint4.o gsnap_sse42-indexdb.o gsnap_sse42-localdb-read.o gsnap_sse42-oligo.o gsnap_sse42-chrnum.o gsnap_sse42-maxent_hr.o gsnap_sse42-mapq.o gsnap_sse42-fopen.o gsnap_sse42-shortread.o gsnap_sse42-junction.o gsnap_sse42-concordance.o gsnap_sse42-simplepair.o gsnap_sse42-orderstat.o gsnap_sse42-intlistpool.o gsnap_sse42-uintlistpool.o gsnap_sse42-listpool.o gsnap_sse42-hitlistpool.o gsnap_sse42-pathpool.o gsnap_sse42-auxinfopool.o gsnap_sse42-pathstorepool.o gsnap_sse42-intron.o gsnap_sse42-gbuffer.o gsnap_sse42-select64-common.o gsnap_sse42-select64-ones.o gsnap_sse42-select64-zeroes.o gsnap_sse42-ef64.o gsnap_sse42-nr-x.o gsnap_sse42-knownsplicing.o gsnap_sse42-knownindels.o gsnap_sse42-splice.o gsnap_sse42-indel.o gsnap_sse42-spliceendsgen.o gsnap_sse42-spliceends.o gsnap_sse42-bitpack64-access.o gsnap_sse42-trdiag.o gsnap_sse42-trdiagpool.o gsnap_sse42-tr-extension-search.o gsnap_sse42-univdiag.o gsnap_sse42-univdiagpool.o gsnap_sse42-sedgesort.o gsnap_sse42-auxinfo.o gsnap_sse42-pathstore.o gsnap_sse42-altsplice.o gsnap_sse42-path.o gsnap_sse42-pathpair.o gsnap_sse42-path-solve.o gsnap_sse42-path-fusion.o gsnap_sse42-path-trim.o gsnap_sse42-path-eval.o gsnap_sse42-pathpair-eval.o gsnap_sse42-path-print-alignment.o gsnap_sse42-path-print-m8.o gsnap_sse42-path-print-sam.o gsnap_sse42-path-learn.o gsnap_sse42-method.o gsnap_sse42-doublelist.o gsnap_sse42-bitvector.o gsnap_sse42-transcriptpool.o gsnap_sse42-exon.o gsnap_sse42-transcript.o gsnap_sse42-trpathpool.o gsnap_sse42-trpath.o gsnap_sse42-trpath-solve.o gsnap_sse42-trpath-convert.o gsnap_sse42-trpath-eval.o gsnap_sse42-transcriptome-search.o gsnap_sse42-vectorpool.o gsnap_sse42-repair.o gsnap_sse42-transcript-remap.o gsnap_sse42-transcript-velocity.o gsnap_sse42-intersect-small.o gsnap_sse42-intersect-uint2.o gsnap_sse42-intersect-approx-uint4.o gsnap_sse42-intersect-approx-indices-uint4.o gsnap_sse42-intersect-wdups-indices.o gsnap_sse42-intersect-lower-small.o gsnap_sse42-intersect-higher-small.o gsnap_sse42-intersect-indices-small.o gsnap_sse42-intersect-indices2-small.o gsnap_sse42-intersect-concordance-uint4.o gsnap_sse42-kmer-search.o gsnap_sse42-extension-search.o gsnap_sse42-repetitive.o gsnap_sse42-uint8table.o gsnap_sse42-uinttable.o gsnap_sse42-stage1hr.o gsnap_sse42-stage1hr-single.o gsnap_sse42-stage1hr-paired.o gsnap_sse42-uinttableuint.o gsnap_sse42-tableuint.o gsnap_sse42-single-cell.o gsnap_sse42-request.o gsnap_sse42-resulthr.o gsnap_sse42-output.o gsnap_sse42-inbuffer.o gsnap_sse42-samheader.o gsnap_sse42-printbuffer.o gsnap_sse42-outbuffer.o gsnap_sse42-uintpairtable.o gsnap_sse42-splice-count.o gsnap_sse42-support.o gsnap_sse42-datadir.o gsnap_sse42-parserange.o gsnap_sse42-getline.o gsnap_sse42-gsnap.o -lz -lbz2 -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse42 gsnapl_sse42-except.o gsnapl_sse42-assert.o gsnapl_sse42-mem.o gsnapl_sse42-intlist.o gsnapl_sse42-uintlist.o gsnapl_sse42-uint8list.o gsnapl_sse42-list.o gsnapl_sse42-littleendian.o gsnapl_sse42-bigendian.o gsnapl_sse42-univinterval.o gsnapl_sse42-interval.o gsnapl_sse42-stopwatch.o gsnapl_sse42-semaphore.o gsnapl_sse42-access.o gsnapl_sse42-filestring.o gsnapl_sse42-iit-read-univ.o gsnapl_sse42-iit-read.o gsnapl_sse42-bzip2.o gsnapl_sse42-reader.o gsnapl_sse42-genomicpos.o gsnapl_sse42-compress.o gsnapl_sse42-genome.o gsnapl_sse42-transcriptome.o gsnapl_sse42-popcount.o gsnapl_sse42-genomebits.o gsnapl_sse42-genomebits_consec.o gsnapl_sse42-genomebits_count.o gsnapl_sse42-genomebits_kmer.o gsnapl_sse42-genomebits_indel.o gsnapl_sse42-genomebits_decode.o gsnapl_sse42-genomebits_mismatches.o gsnapl_sse42-genomebits_trim.o gsnapl_sse42-dinucl_bits.o gsnapl_sse42-genome_sites.o gsnapl_sse42-bitpack64-read.o gsnapl_sse42-bitpack64-readtwo.o gsnapl_sse42-mergeinfo.o gsnapl_sse42-merge-diagonals-heap-uint8.o gsnapl_sse42-merge-uint8.o gsnapl_sse42-merge-diagonals-simd-uint8.o gsnapl_sse42-merge-diagonals-heap-uint4.o gsnapl_sse42-merge-uint4.o gsnapl_sse42-merge-diagonals-simd-uint4.o gsnapl_sse42-indexdb.o gsnapl_sse42-localdb-read.o gsnapl_sse42-oligo.o gsnapl_sse42-chrnum.o gsnapl_sse42-maxent_hr.o gsnapl_sse42-mapq.o gsnapl_sse42-fopen.o gsnapl_sse42-shortread.o gsnapl_sse42-junction.o gsnapl_sse42-concordance.o gsnapl_sse42-simplepair.o gsnapl_sse42-orderstat.o gsnapl_sse42-intlistpool.o gsnapl_sse42-uintlistpool.o gsnapl_sse42-uint8listpool.o gsnapl_sse42-listpool.o gsnapl_sse42-hitlistpool.o gsnapl_sse42-pathpool.o gsnapl_sse42-auxinfopool.o gsnapl_sse42-pathstorepool.o gsnapl_sse42-intron.o gsnapl_sse42-gbuffer.o gsnapl_sse42-select64-common.o gsnapl_sse42-select64-ones.o gsnapl_sse42-select64-zeroes.o gsnapl_sse42-ef64.o gsnapl_sse42-nr-x.o gsnapl_sse42-knownsplicing.o gsnapl_sse42-knownindels.o gsnapl_sse42-splice.o gsnapl_sse42-indel.o gsnapl_sse42-spliceendsgen.o gsnapl_sse42-spliceends.o gsnapl_sse42-bitpack64-access.o gsnapl_sse42-trdiag.o gsnapl_sse42-trdiagpool.o gsnapl_sse42-tr-extension-search.o gsnapl_sse42-univdiag.o gsnapl_sse42-univdiagpool.o gsnapl_sse42-sedgesort.o gsnapl_sse42-auxinfo.o gsnapl_sse42-pathstore.o gsnapl_sse42-altsplice.o gsnapl_sse42-path.o gsnapl_sse42-pathpair.o gsnapl_sse42-path-solve.o gsnapl_sse42-path-fusion.o gsnapl_sse42-path-trim.o gsnapl_sse42-path-eval.o gsnapl_sse42-pathpair-eval.o gsnapl_sse42-path-print-alignment.o gsnapl_sse42-path-print-m8.o gsnapl_sse42-path-print-sam.o gsnapl_sse42-path-learn.o gsnapl_sse42-method.o gsnapl_sse42-doublelist.o gsnapl_sse42-bitvector.o gsnapl_sse42-transcriptpool.o gsnapl_sse42-exon.o gsnapl_sse42-transcript.o gsnapl_sse42-trpathpool.o gsnapl_sse42-trpath.o gsnapl_sse42-trpath-solve.o gsnapl_sse42-trpath-convert.o gsnapl_sse42-trpath-eval.o gsnapl_sse42-transcriptome-search.o gsnapl_sse42-vectorpool.o gsnapl_sse42-repair.o gsnapl_sse42-transcript-remap.o gsnapl_sse42-transcript-velocity.o gsnapl_sse42-intersect-large.o gsnapl_sse42-intersect-small.o gsnapl_sse42-intersect-uint2.o gsnapl_sse42-intersect-approx-uint4.o gsnapl_sse42-intersect-approx-uint8.o gsnapl_sse42-intersect-approx-indices-uint8.o gsnapl_sse42-intersect-wdups-indices.o gsnapl_sse42-intersect-lower-large.o gsnapl_sse42-intersect-higher-large.o gsnapl_sse42-intersect-indices-small.o gsnapl_sse42-intersect-indices2-large.o gsnapl_sse42-intersect-indices-uint8.o gsnapl_sse42-intersect-concordance-uint8.o gsnapl_sse42-kmer-search.o gsnapl_sse42-extension-search.o gsnapl_sse42-repetitive.o gsnapl_sse42-uint8table.o gsnapl_sse42-stage1hr.o gsnapl_sse42-stage1hr-single.o gsnapl_sse42-stage1hr-paired.o gsnapl_sse42-uint8tableuint.o gsnapl_sse42-tableuint.o gsnapl_sse42-single-cell.o gsnapl_sse42-request.o gsnapl_sse42-resulthr.o gsnapl_sse42-output.o gsnapl_sse42-inbuffer.o gsnapl_sse42-samheader.o gsnapl_sse42-printbuffer.o gsnapl_sse42-outbuffer.o gsnapl_sse42-uint8pairtable.o gsnapl_sse42-splice-count.o gsnapl_sse42-support.o gsnapl_sse42-datadir.o gsnapl_sse42-parserange.o gsnapl_sse42-getline.o gsnapl_sse42-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites chmod +x gmap_process cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x gmap_build chmod +x gmap_cat chmod +x md_coords chmod +x fa_coords chmod +x psl_splicesites cp ensembl_genes.pl ensembl_genes chmod +x psl_introns chmod +x psl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x ensembl_genes cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gtf_splicesites cp gff3_genes.pl gff3_genes chmod +x gtf_introns chmod +x gtf_genes chmod +x gtf_transcript_splicesites cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_splicesites chmod +x gff3_introns chmod +x gff3_genes cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x dbsnp_iit chmod +x vcf_iit chmod +x gvf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' dh_auto_build --builddir build_avx2 cd build_avx2 && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-dinucl_bits.o gmap_avx2-genome_canonical.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-printbuffer.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-dinucl_bits.o gmapl_avx2-genome_canonical.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-uint8table_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-printbuffer.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genomebits.o gsnap_avx2-genomebits_consec.o gsnap_avx2-genomebits_count.o gsnap_avx2-genomebits_kmer.o gsnap_avx2-genomebits_indel.o gsnap_avx2-genomebits_decode.o gsnap_avx2-genomebits_mismatches.o gsnap_avx2-genomebits_trim.o gsnap_avx2-dinucl_bits.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-mergeinfo.o gsnap_avx2-merge-diagonals-heap-uint4.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-localdb-read.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-junction.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-pathpool.o gsnap_avx2-auxinfopool.o gsnap_avx2-pathstorepool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-select64-common.o gsnap_avx2-select64-ones.o gsnap_avx2-select64-zeroes.o gsnap_avx2-ef64.o gsnap_avx2-nr-x.o gsnap_avx2-knownsplicing.o gsnap_avx2-knownindels.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-spliceendsgen.o gsnap_avx2-spliceends.o gsnap_avx2-bitpack64-access.o gsnap_avx2-trdiag.o gsnap_avx2-trdiagpool.o gsnap_avx2-tr-extension-search.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-auxinfo.o gsnap_avx2-pathstore.o gsnap_avx2-altsplice.o gsnap_avx2-path.o gsnap_avx2-pathpair.o gsnap_avx2-path-solve.o gsnap_avx2-path-fusion.o gsnap_avx2-path-trim.o gsnap_avx2-path-eval.o gsnap_avx2-pathpair-eval.o gsnap_avx2-path-print-alignment.o gsnap_avx2-path-print-m8.o gsnap_avx2-path-print-sam.o gsnap_avx2-path-learn.o gsnap_avx2-method.o gsnap_avx2-doublelist.o gsnap_avx2-bitvector.o gsnap_avx2-transcriptpool.o gsnap_avx2-exon.o gsnap_avx2-transcript.o gsnap_avx2-trpathpool.o gsnap_avx2-trpath.o gsnap_avx2-trpath-solve.o gsnap_avx2-trpath-convert.o gsnap_avx2-trpath-eval.o gsnap_avx2-transcriptome-search.o gsnap_avx2-vectorpool.o gsnap_avx2-repair.o gsnap_avx2-transcript-remap.o gsnap_avx2-transcript-velocity.o gsnap_avx2-intersect-small.o gsnap_avx2-intersect-uint2.o gsnap_avx2-intersect-approx-uint4.o gsnap_avx2-intersect-approx-indices-uint4.o gsnap_avx2-intersect-wdups-indices.o gsnap_avx2-intersect-lower-small.o gsnap_avx2-intersect-higher-small.o gsnap_avx2-intersect-indices-small.o gsnap_avx2-intersect-indices2-small.o gsnap_avx2-intersect-concordance-uint4.o gsnap_avx2-kmer-search.o gsnap_avx2-extension-search.o gsnap_avx2-repetitive.o gsnap_avx2-uint8table.o gsnap_avx2-uinttable.o gsnap_avx2-stage1hr.o gsnap_avx2-stage1hr-single.o gsnap_avx2-stage1hr-paired.o gsnap_avx2-uinttableuint.o gsnap_avx2-tableuint.o gsnap_avx2-single-cell.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-printbuffer.o gsnap_avx2-outbuffer.o gsnap_avx2-uintpairtable.o gsnap_avx2-splice-count.o gsnap_avx2-support.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-gsnap.o -lz -lbz2 -lm ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx2 gsnapl_avx2-except.o gsnapl_avx2-assert.o gsnapl_avx2-mem.o gsnapl_avx2-intlist.o gsnapl_avx2-uintlist.o gsnapl_avx2-uint8list.o gsnapl_avx2-list.o gsnapl_avx2-littleendian.o gsnapl_avx2-bigendian.o gsnapl_avx2-univinterval.o gsnapl_avx2-interval.o gsnapl_avx2-stopwatch.o gsnapl_avx2-semaphore.o gsnapl_avx2-access.o gsnapl_avx2-filestring.o gsnapl_avx2-iit-read-univ.o gsnapl_avx2-iit-read.o gsnapl_avx2-bzip2.o gsnapl_avx2-reader.o gsnapl_avx2-genomicpos.o gsnapl_avx2-compress.o gsnapl_avx2-genome.o gsnapl_avx2-transcriptome.o gsnapl_avx2-popcount.o gsnapl_avx2-genomebits.o gsnapl_avx2-genomebits_consec.o gsnapl_avx2-genomebits_count.o gsnapl_avx2-genomebits_kmer.o gsnapl_avx2-genomebits_indel.o gsnapl_avx2-genomebits_decode.o gsnapl_avx2-genomebits_mismatches.o gsnapl_avx2-genomebits_trim.o gsnapl_avx2-dinucl_bits.o gsnapl_avx2-genome_sites.o gsnapl_avx2-bitpack64-read.o gsnapl_avx2-bitpack64-readtwo.o gsnapl_avx2-mergeinfo.o gsnapl_avx2-merge-diagonals-heap-uint8.o gsnapl_avx2-merge-uint8.o gsnapl_avx2-merge-diagonals-simd-uint8.o gsnapl_avx2-merge-diagonals-heap-uint4.o gsnapl_avx2-merge-uint4.o gsnapl_avx2-merge-diagonals-simd-uint4.o gsnapl_avx2-indexdb.o gsnapl_avx2-localdb-read.o gsnapl_avx2-oligo.o gsnapl_avx2-chrnum.o gsnapl_avx2-maxent_hr.o gsnapl_avx2-mapq.o gsnapl_avx2-fopen.o gsnapl_avx2-shortread.o gsnapl_avx2-junction.o gsnapl_avx2-concordance.o gsnapl_avx2-simplepair.o gsnapl_avx2-orderstat.o gsnapl_avx2-intlistpool.o gsnapl_avx2-uintlistpool.o gsnapl_avx2-uint8listpool.o gsnapl_avx2-listpool.o gsnapl_avx2-hitlistpool.o gsnapl_avx2-pathpool.o gsnapl_avx2-auxinfopool.o gsnapl_avx2-pathstorepool.o gsnapl_avx2-intron.o gsnapl_avx2-gbuffer.o gsnapl_avx2-select64-common.o gsnapl_avx2-select64-ones.o gsnapl_avx2-select64-zeroes.o gsnapl_avx2-ef64.o gsnapl_avx2-nr-x.o gsnapl_avx2-knownsplicing.o gsnapl_avx2-knownindels.o gsnapl_avx2-splice.o gsnapl_avx2-indel.o gsnapl_avx2-spliceendsgen.o gsnapl_avx2-spliceends.o gsnapl_avx2-bitpack64-access.o gsnapl_avx2-trdiag.o gsnapl_avx2-trdiagpool.o gsnapl_avx2-tr-extension-search.o gsnapl_avx2-univdiag.o gsnapl_avx2-univdiagpool.o gsnapl_avx2-sedgesort.o gsnapl_avx2-auxinfo.o gsnapl_avx2-pathstore.o gsnapl_avx2-altsplice.o gsnapl_avx2-path.o gsnapl_avx2-pathpair.o gsnapl_avx2-path-solve.o gsnapl_avx2-path-fusion.o gsnapl_avx2-path-trim.o gsnapl_avx2-path-eval.o gsnapl_avx2-pathpair-eval.o gsnapl_avx2-path-print-alignment.o gsnapl_avx2-path-print-m8.o gsnapl_avx2-path-print-sam.o gsnapl_avx2-path-learn.o gsnapl_avx2-method.o gsnapl_avx2-doublelist.o gsnapl_avx2-bitvector.o gsnapl_avx2-transcriptpool.o gsnapl_avx2-exon.o gsnapl_avx2-transcript.o gsnapl_avx2-trpathpool.o gsnapl_avx2-trpath.o gsnapl_avx2-trpath-solve.o gsnapl_avx2-trpath-convert.o gsnapl_avx2-trpath-eval.o gsnapl_avx2-transcriptome-search.o gsnapl_avx2-vectorpool.o gsnapl_avx2-repair.o gsnapl_avx2-transcript-remap.o gsnapl_avx2-transcript-velocity.o gsnapl_avx2-intersect-large.o gsnapl_avx2-intersect-small.o gsnapl_avx2-intersect-uint2.o gsnapl_avx2-intersect-approx-uint4.o gsnapl_avx2-intersect-approx-uint8.o gsnapl_avx2-intersect-approx-indices-uint8.o gsnapl_avx2-intersect-wdups-indices.o gsnapl_avx2-intersect-lower-large.o gsnapl_avx2-intersect-higher-large.o gsnapl_avx2-intersect-indices-small.o gsnapl_avx2-intersect-indices2-large.o gsnapl_avx2-intersect-indices-uint8.o gsnapl_avx2-intersect-concordance-uint8.o gsnapl_avx2-kmer-search.o gsnapl_avx2-extension-search.o gsnapl_avx2-repetitive.o gsnapl_avx2-uint8table.o gsnapl_avx2-stage1hr.o gsnapl_avx2-stage1hr-single.o gsnapl_avx2-stage1hr-paired.o gsnapl_avx2-uint8tableuint.o gsnapl_avx2-tableuint.o gsnapl_avx2-single-cell.o gsnapl_avx2-request.o gsnapl_avx2-resulthr.o gsnapl_avx2-output.o gsnapl_avx2-inbuffer.o gsnapl_avx2-samheader.o gsnapl_avx2-printbuffer.o gsnapl_avx2-outbuffer.o gsnapl_avx2-uint8pairtable.o gsnapl_avx2-splice-count.o gsnapl_avx2-support.o gsnapl_avx2-datadir.o gsnapl_avx2-parserange.o gsnapl_avx2-getline.o gsnapl_avx2-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x fa_coords cp ensembl_genes.pl ensembl_genes chmod +x psl_splicesites chmod +x psl_introns chmod +x psl_genes chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_introns chmod +x gtf_transcript_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites chmod +x gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x dbsnp_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' dh_auto_build --builddir build_avx512 cd build_avx512 && make -j42 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx512 gmap_avx512-except.o gmap_avx512-assert.o gmap_avx512-mem.o gmap_avx512-intlist.o gmap_avx512-uintlist.o gmap_avx512-list.o gmap_avx512-littleendian.o gmap_avx512-bigendian.o gmap_avx512-univinterval.o gmap_avx512-interval.o gmap_avx512-stopwatch.o gmap_avx512-semaphore.o gmap_avx512-access.o gmap_avx512-filestring.o gmap_avx512-iit-read-univ.o gmap_avx512-iit-read.o gmap_avx512-md5.o gmap_avx512-bzip2.o gmap_avx512-fopen.o gmap_avx512-sequence.o gmap_avx512-reader.o gmap_avx512-genomicpos.o gmap_avx512-compress.o gmap_avx512-compress-write.o gmap_avx512-gbuffer.o gmap_avx512-genome.o gmap_avx512-popcount.o gmap_avx512-dinucl_bits.o gmap_avx512-genome_canonical.o gmap_avx512-genome-write.o gmap_avx512-bitpack64-read.o gmap_avx512-bitpack64-readtwo.o gmap_avx512-indexdb.o gmap_avx512-oligo.o gmap_avx512-block.o gmap_avx512-chrom.o gmap_avx512-segmentpos.o gmap_avx512-chrnum.o gmap_avx512-uinttable_rh.o gmap_avx512-gregion.o gmap_avx512-match.o gmap_avx512-matchpool.o gmap_avx512-diagnostic.o gmap_avx512-stage1.o gmap_avx512-diag.o gmap_avx512-diagpool.o gmap_avx512-cmet.o gmap_avx512-atoi.o gmap_avx512-orderstat.o gmap_avx512-oligoindex_hr.o gmap_avx512-intron.o gmap_avx512-maxent.o gmap_avx512-maxent_hr.o gmap_avx512-pair.o gmap_avx512-pairpool.o gmap_avx512-cellpool.o gmap_avx512-stage2.o gmap_avx512-doublelist.o gmap_avx512-smooth.o gmap_avx512-splicestringpool.o gmap_avx512-splicetrie_build.o gmap_avx512-splicetrie.o gmap_avx512-boyer-moore.o gmap_avx512-dynprog.o gmap_avx512-dynprog_simd.o gmap_avx512-dynprog_single.o gmap_avx512-dynprog_genome.o gmap_avx512-dynprog_cdna.o gmap_avx512-dynprog_end.o gmap_avx512-translation.o gmap_avx512-pbinom.o gmap_avx512-changepoint.o gmap_avx512-stage3.o gmap_avx512-request.o gmap_avx512-result.o gmap_avx512-output.o gmap_avx512-inbuffer.o gmap_avx512-samheader.o gmap_avx512-printbuffer.o gmap_avx512-outbuffer.o gmap_avx512-chimera.o gmap_avx512-datadir.o gmap_avx512-parserange.o gmap_avx512-getline.o gmap_avx512-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx512 gsnap_avx512-except.o gsnap_avx512-assert.o gsnap_avx512-mem.o gsnap_avx512-intlist.o gsnap_avx512-uintlist.o gsnap_avx512-list.o gsnap_avx512-littleendian.o gsnap_avx512-bigendian.o gsnap_avx512-univinterval.o gsnap_avx512-interval.o gsnap_avx512-stopwatch.o gsnap_avx512-semaphore.o gsnap_avx512-access.o gsnap_avx512-filestring.o gsnap_avx512-iit-read-univ.o gsnap_avx512-iit-read.o gsnap_avx512-bzip2.o gsnap_avx512-reader.o gsnap_avx512-genomicpos.o gsnap_avx512-compress.o gsnap_avx512-genome.o gsnap_avx512-transcriptome.o gsnap_avx512-popcount.o gsnap_avx512-genomebits.o gsnap_avx512-genomebits_consec.o gsnap_avx512-genomebits_count.o gsnap_avx512-genomebits_kmer.o gsnap_avx512-genomebits_indel.o gsnap_avx512-genomebits_decode.o gsnap_avx512-genomebits_mismatches.o gsnap_avx512-genomebits_trim.o gsnap_avx512-dinucl_bits.o gsnap_avx512-genome_sites.o gsnap_avx512-bitpack64-read.o gsnap_avx512-bitpack64-readtwo.o gsnap_avx512-mergeinfo.o gsnap_avx512-merge-diagonals-heap-uint4.o gsnap_avx512-merge-uint4.o gsnap_avx512-merge-diagonals-simd-uint4.o gsnap_avx512-indexdb.o gsnap_avx512-localdb-read.o gsnap_avx512-oligo.o gsnap_avx512-chrnum.o gsnap_avx512-maxent_hr.o gsnap_avx512-mapq.o gsnap_avx512-fopen.o gsnap_avx512-shortread.o gsnap_avx512-junction.o gsnap_avx512-concordance.o gsnap_avx512-simplepair.o gsnap_avx512-orderstat.o gsnap_avx512-intlistpool.o gsnap_avx512-uintlistpool.o gsnap_avx512-listpool.o gsnap_avx512-hitlistpool.o gsnap_avx512-pathpool.o gsnap_avx512-auxinfopool.o gsnap_avx512-pathstorepool.o gsnap_avx512-intron.o gsnap_avx512-gbuffer.o gsnap_avx512-select64-common.o gsnap_avx512-select64-ones.o gsnap_avx512-select64-zeroes.o gsnap_avx512-ef64.o gsnap_avx512-nr-x.o gsnap_avx512-knownsplicing.o gsnap_avx512-knownindels.o gsnap_avx512-splice.o gsnap_avx512-indel.o gsnap_avx512-spliceendsgen.o gsnap_avx512-spliceends.o gsnap_avx512-bitpack64-access.o gsnap_avx512-trdiag.o gsnap_avx512-trdiagpool.o gsnap_avx512-tr-extension-search.o gsnap_avx512-univdiag.o gsnap_avx512-univdiagpool.o gsnap_avx512-sedgesort.o gsnap_avx512-auxinfo.o gsnap_avx512-pathstore.o gsnap_avx512-altsplice.o gsnap_avx512-path.o gsnap_avx512-pathpair.o gsnap_avx512-path-solve.o gsnap_avx512-path-fusion.o gsnap_avx512-path-trim.o gsnap_avx512-path-eval.o gsnap_avx512-pathpair-eval.o gsnap_avx512-path-print-alignment.o gsnap_avx512-path-print-m8.o gsnap_avx512-path-print-sam.o gsnap_avx512-path-learn.o gsnap_avx512-method.o gsnap_avx512-doublelist.o gsnap_avx512-bitvector.o gsnap_avx512-transcriptpool.o gsnap_avx512-exon.o gsnap_avx512-transcript.o gsnap_avx512-trpathpool.o gsnap_avx512-trpath.o gsnap_avx512-trpath-solve.o gsnap_avx512-trpath-convert.o gsnap_avx512-trpath-eval.o gsnap_avx512-transcriptome-search.o gsnap_avx512-vectorpool.o gsnap_avx512-repair.o gsnap_avx512-transcript-remap.o gsnap_avx512-transcript-velocity.o gsnap_avx512-intersect-small.o gsnap_avx512-intersect-uint2.o gsnap_avx512-intersect-approx-uint4.o gsnap_avx512-intersect-approx-indices-uint4.o gsnap_avx512-intersect-wdups-indices.o gsnap_avx512-intersect-lower-small.o gsnap_avx512-intersect-higher-small.o gsnap_avx512-intersect-indices-small.o gsnap_avx512-intersect-indices2-small.o gsnap_avx512-intersect-concordance-uint4.o gsnap_avx512-kmer-search.o gsnap_avx512-extension-search.o gsnap_avx512-repetitive.o gsnap_avx512-uint8table.o gsnap_avx512-uinttable.o gsnap_avx512-stage1hr.o gsnap_avx512-stage1hr-single.o gsnap_avx512-stage1hr-paired.o gsnap_avx512-uinttableuint.o gsnap_avx512-tableuint.o gsnap_avx512-single-cell.o gsnap_avx512-request.o gsnap_avx512-resulthr.o gsnap_avx512-output.o gsnap_avx512-inbuffer.o gsnap_avx512-samheader.o gsnap_avx512-printbuffer.o gsnap_avx512-outbuffer.o gsnap_avx512-uintpairtable.o gsnap_avx512-splice-count.o gsnap_avx512-support.o gsnap_avx512-datadir.o gsnap_avx512-parserange.o gsnap_avx512-getline.o gsnap_avx512-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx512 gmapl_avx512-except.o gmapl_avx512-assert.o gmapl_avx512-mem.o gmapl_avx512-intlist.o gmapl_avx512-uintlist.o gmapl_avx512-uint8list.o gmapl_avx512-list.o gmapl_avx512-littleendian.o gmapl_avx512-bigendian.o gmapl_avx512-univinterval.o gmapl_avx512-interval.o gmapl_avx512-stopwatch.o gmapl_avx512-semaphore.o gmapl_avx512-access.o gmapl_avx512-filestring.o gmapl_avx512-iit-read-univ.o gmapl_avx512-iit-read.o gmapl_avx512-md5.o gmapl_avx512-bzip2.o gmapl_avx512-fopen.o gmapl_avx512-sequence.o gmapl_avx512-reader.o gmapl_avx512-genomicpos.o gmapl_avx512-compress.o gmapl_avx512-compress-write.o gmapl_avx512-gbuffer.o gmapl_avx512-genome.o gmapl_avx512-popcount.o gmapl_avx512-dinucl_bits.o gmapl_avx512-genome_canonical.o gmapl_avx512-genome-write.o gmapl_avx512-bitpack64-read.o gmapl_avx512-bitpack64-readtwo.o gmapl_avx512-indexdb.o gmapl_avx512-oligo.o gmapl_avx512-block.o gmapl_avx512-chrom.o gmapl_avx512-segmentpos.o gmapl_avx512-chrnum.o gmapl_avx512-uinttable_rh.o gmapl_avx512-uint8table_rh.o gmapl_avx512-gregion.o gmapl_avx512-match.o gmapl_avx512-matchpool.o gmapl_avx512-diagnostic.o gmapl_avx512-stage1.o gmapl_avx512-diag.o gmapl_avx512-diagpool.o gmapl_avx512-cmet.o gmapl_avx512-atoi.o gmapl_avx512-orderstat.o gmapl_avx512-oligoindex_hr.o gmapl_avx512-intron.o gmapl_avx512-maxent.o gmapl_avx512-maxent_hr.o gmapl_avx512-pair.o gmapl_avx512-pairpool.o gmapl_avx512-cellpool.o gmapl_avx512-stage2.o gmapl_avx512-doublelist.o gmapl_avx512-smooth.o gmapl_avx512-splicestringpool.o gmapl_avx512-splicetrie_build.o gmapl_avx512-splicetrie.o gmapl_avx512-boyer-moore.o gmapl_avx512-dynprog.o gmapl_avx512-dynprog_simd.o gmapl_avx512-dynprog_single.o gmapl_avx512-dynprog_genome.o gmapl_avx512-dynprog_cdna.o gmapl_avx512-dynprog_end.o gmapl_avx512-translation.o gmapl_avx512-pbinom.o gmapl_avx512-changepoint.o gmapl_avx512-stage3.o gmapl_avx512-request.o gmapl_avx512-result.o gmapl_avx512-output.o gmapl_avx512-inbuffer.o gmapl_avx512-samheader.o gmapl_avx512-printbuffer.o gmapl_avx512-outbuffer.o gmapl_avx512-chimera.o gmapl_avx512-datadir.o gmapl_avx512-parserange.o gmapl_avx512-getline.o gmapl_avx512-gmap.o -lz -lbz2 -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx512 gsnapl_avx512-except.o gsnapl_avx512-assert.o gsnapl_avx512-mem.o gsnapl_avx512-intlist.o gsnapl_avx512-uintlist.o gsnapl_avx512-uint8list.o gsnapl_avx512-list.o gsnapl_avx512-littleendian.o gsnapl_avx512-bigendian.o gsnapl_avx512-univinterval.o gsnapl_avx512-interval.o gsnapl_avx512-stopwatch.o gsnapl_avx512-semaphore.o gsnapl_avx512-access.o gsnapl_avx512-filestring.o gsnapl_avx512-iit-read-univ.o gsnapl_avx512-iit-read.o gsnapl_avx512-bzip2.o gsnapl_avx512-reader.o gsnapl_avx512-genomicpos.o gsnapl_avx512-compress.o gsnapl_avx512-genome.o gsnapl_avx512-transcriptome.o gsnapl_avx512-popcount.o gsnapl_avx512-genomebits.o gsnapl_avx512-genomebits_consec.o gsnapl_avx512-genomebits_count.o gsnapl_avx512-genomebits_kmer.o gsnapl_avx512-genomebits_indel.o gsnapl_avx512-genomebits_decode.o gsnapl_avx512-genomebits_mismatches.o gsnapl_avx512-genomebits_trim.o gsnapl_avx512-dinucl_bits.o gsnapl_avx512-genome_sites.o gsnapl_avx512-bitpack64-read.o gsnapl_avx512-bitpack64-readtwo.o gsnapl_avx512-mergeinfo.o gsnapl_avx512-merge-diagonals-heap-uint8.o gsnapl_avx512-merge-uint8.o gsnapl_avx512-merge-diagonals-simd-uint8.o gsnapl_avx512-merge-diagonals-heap-uint4.o gsnapl_avx512-merge-uint4.o gsnapl_avx512-merge-diagonals-simd-uint4.o gsnapl_avx512-indexdb.o gsnapl_avx512-localdb-read.o gsnapl_avx512-oligo.o gsnapl_avx512-chrnum.o gsnapl_avx512-maxent_hr.o gsnapl_avx512-mapq.o gsnapl_avx512-fopen.o gsnapl_avx512-shortread.o gsnapl_avx512-junction.o gsnapl_avx512-concordance.o gsnapl_avx512-simplepair.o gsnapl_avx512-orderstat.o gsnapl_avx512-intlistpool.o gsnapl_avx512-uintlistpool.o gsnapl_avx512-uint8listpool.o gsnapl_avx512-listpool.o gsnapl_avx512-hitlistpool.o gsnapl_avx512-pathpool.o gsnapl_avx512-auxinfopool.o gsnapl_avx512-pathstorepool.o gsnapl_avx512-intron.o gsnapl_avx512-gbuffer.o gsnapl_avx512-select64-common.o gsnapl_avx512-select64-ones.o gsnapl_avx512-select64-zeroes.o gsnapl_avx512-ef64.o gsnapl_avx512-nr-x.o gsnapl_avx512-knownsplicing.o gsnapl_avx512-knownindels.o gsnapl_avx512-splice.o gsnapl_avx512-indel.o gsnapl_avx512-spliceendsgen.o gsnapl_avx512-spliceends.o gsnapl_avx512-bitpack64-access.o gsnapl_avx512-trdiag.o gsnapl_avx512-trdiagpool.o gsnapl_avx512-tr-extension-search.o gsnapl_avx512-univdiag.o gsnapl_avx512-univdiagpool.o gsnapl_avx512-sedgesort.o gsnapl_avx512-auxinfo.o gsnapl_avx512-pathstore.o gsnapl_avx512-altsplice.o gsnapl_avx512-path.o gsnapl_avx512-pathpair.o gsnapl_avx512-path-solve.o gsnapl_avx512-path-fusion.o gsnapl_avx512-path-trim.o gsnapl_avx512-path-eval.o gsnapl_avx512-pathpair-eval.o gsnapl_avx512-path-print-alignment.o gsnapl_avx512-path-print-m8.o gsnapl_avx512-path-print-sam.o gsnapl_avx512-path-learn.o gsnapl_avx512-method.o gsnapl_avx512-doublelist.o gsnapl_avx512-bitvector.o gsnapl_avx512-transcriptpool.o gsnapl_avx512-exon.o gsnapl_avx512-transcript.o gsnapl_avx512-trpathpool.o gsnapl_avx512-trpath.o gsnapl_avx512-trpath-solve.o gsnapl_avx512-trpath-convert.o gsnapl_avx512-trpath-eval.o gsnapl_avx512-transcriptome-search.o gsnapl_avx512-vectorpool.o gsnapl_avx512-repair.o gsnapl_avx512-transcript-remap.o gsnapl_avx512-transcript-velocity.o gsnapl_avx512-intersect-large.o gsnapl_avx512-intersect-small.o gsnapl_avx512-intersect-uint2.o gsnapl_avx512-intersect-approx-uint4.o gsnapl_avx512-intersect-approx-uint8.o gsnapl_avx512-intersect-approx-indices-uint8.o gsnapl_avx512-intersect-wdups-indices.o gsnapl_avx512-intersect-lower-large.o gsnapl_avx512-intersect-higher-large.o gsnapl_avx512-intersect-indices-small.o gsnapl_avx512-intersect-indices2-large.o gsnapl_avx512-intersect-indices-uint8.o gsnapl_avx512-intersect-concordance-uint8.o gsnapl_avx512-kmer-search.o gsnapl_avx512-extension-search.o gsnapl_avx512-repetitive.o gsnapl_avx512-uint8table.o gsnapl_avx512-stage1hr.o gsnapl_avx512-stage1hr-single.o gsnapl_avx512-stage1hr-paired.o gsnapl_avx512-uint8tableuint.o gsnapl_avx512-tableuint.o gsnapl_avx512-single-cell.o gsnapl_avx512-request.o gsnapl_avx512-resulthr.o gsnapl_avx512-output.o gsnapl_avx512-inbuffer.o gsnapl_avx512-samheader.o gsnapl_avx512-printbuffer.o gsnapl_avx512-outbuffer.o gsnapl_avx512-uint8pairtable.o gsnapl_avx512-splice-count.o gsnapl_avx512-support.o gsnapl_avx512-datadir.o gsnapl_avx512-parserange.o gsnapl_avx512-getline.o gsnapl_avx512-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes chmod +x md_coords chmod +x fa_coords chmod +x psl_splicesites chmod +x psl_introns cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x psl_genes cp gtf_genes.pl gtf_genes chmod +x ensembl_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns cp gff3_genes.pl gff3_genes chmod +x gtf_splicesites chmod +x gtf_introns chmod +x gtf_genes cp dbsnp_iit.pl dbsnp_iit chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites chmod +x gff3_introns cp gvf_iit.pl gvf_iit chmod +x gff3_genes cp vcf_iit.pl vcf_iit chmod +x dbsnp_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_test --no-parallel cd build && make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making check in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' Making check in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making check in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make check-TESTS make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[5]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' PASS: align.test PASS: coords1.test PASS: setup1.test PASS: iit.test ============================================================================ Testsuite summary for gmap 2024-11-20 ============================================================================ # TOTAL: 4 # PASS: 4 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--builddir=build dh_prep -O--builddir=build debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' mkdir -p /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Genomic Mapping and Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gmap |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Genomic Short-read Nucleotide Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gsnap |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gsnap.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Large Genome Mapping and Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gmapl |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmapl.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Large Genome Short-read Nucleotide Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gsnapl |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gsnapl.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Tool for genome database creation for GMAP or GSNAP' \ /build/reproducible-path/gmap-2024-11-20+ds/build/util/gmap_build |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap_build.1 dh_auto_install --builddir build_avx512 cd build_avx512 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx512 gmapl.avx512 gsnap.avx512 gsnapl.avx512 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' dh_auto_install --builddir build_avx2 cd build_avx2 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx2 gmapl.avx2 gsnap.avx2 gsnapl.avx2 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' dh_auto_install --builddir build_sse42 cd build_sse42 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse42 gmapl.sse42 gsnap.sse42 gsnapl.sse42 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' dh_auto_install --builddir build_sse41 cd build_sse41 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse41 gmapl.sse41 gsnap.sse41 gsnapl.sse41 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' dh_auto_install --builddir build_ssse3 cd build_ssse3 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.ssse3 gmapl.ssse3 gsnap.ssse3 gsnapl.ssse3 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' dh_auto_install cd build && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse2 gmapl.sse2 gsnap.sse2 gsnapl.sse2 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' mkdir -p debian/gmap/usr/bin dh_install for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \ cd /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap/; \ ls -1 gmap*.* gsnap*.* `; do \ ln -s /usr/lib/gmap/$bin debian/gmap/usr/bin/$bin; \ done make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_installdocs -O--builddir=build dh_installchangelogs -O--builddir=build debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' mkdir /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/doc/gmap/examples find tests/ -type f -print0 | xargs -0r sed -i \ -e 's@/build/reproducible-path/gmap-2024-11-20+ds@«buildpath»@g' \ -e 's@\#! /bin/bash@\#! /bin/sh@g' tar --sort=name \ --mtime="@1740521462" \ --owner=root --group=root --numeric-owner \ --mode=go=rX,u+rw,a-s \ --exclude='*/align.log' \ --exclude='*/Makefile' \ --exclude='*/Makefile.in' \ -cJf /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/doc/gmap/examples/tests.tar.xz tests make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_installman -O--builddir=build dh_installsystemduser -O--builddir=build dh_lintian -O--builddir=build dh_perl -O--builddir=build dh_link -O--builddir=build dh_strip_nondeterminism -O--builddir=build dh_compress -O--builddir=build dh_fixperms -O--builddir=build dh_missing -O--builddir=build dh_dwz -a -O--builddir=build dh_strip -a -O--builddir=build dh_makeshlibs -a -O--builddir=build dh_shlibdeps -a -O--builddir=build dh_installdeb -O--builddir=build dh_gencontrol -O--builddir=build dh_md5sums -O--builddir=build dh_builddeb -O--builddir=build dpkg-deb: building package 'gmap' in '../gmap_2024-11-20+ds-2_amd64.deb'. dpkg-deb: building package 'gmap-dbgsym' in '../gmap-dbgsym_2024-11-20+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gmap_2024-11-20+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gmap_2024-11-20+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2740700 and its subdirectories I: Current time: Wed Oct 21 09:21:56 -12 2026 I: pbuilder-time-stamp: 1792617716 Thu Sep 18 14:58:57 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu Sep 18 14:58:57 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu Sep 18 14:58:57 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Sep 18 14:58:57 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-tErNNZ' ==================================================================================== Thu Sep 18 14:58:58 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "2 gmap forky /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI 2024-11-20+ds-2" as arguments. Thu Sep 18 14:58:58 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-rVToKoE0" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 14:58:58 UTC 2025 I: Downloading source for forky/gmap=2024-11-20+ds-2 Reading package lists... NOTICE: 'gmap' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gmap.git Please use: git clone https://salsa.debian.org/med-team/gmap.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2595 kB of source archives. Get:1 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (dsc) [2309 B] Get:2 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (tar) [2579 kB] Get:3 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (diff) [14.1 kB] Fetched 2595 kB in 0s (40.8 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'gmap' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gmap.git Please use: git clone https://salsa.debian.org/med-team/gmap.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2595 kB of source archives. Get:1 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (dsc) [2309 B] Get:2 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (tar) [2579 kB] Get:3 http://deb.debian.org/debian forky/main gmap 2024-11-20+ds-2 (diff) [14.1 kB] Fetched 2595 kB in 0s (40.8 MB/s) Download complete and in download only mode ============================================================================= Re-Building gmap in forky on amd64 on ionos1-amd64 now. Date: Thu Sep 18 14:58:59 UTC 2025 Date UTC: Thu Sep 18 14:58:59 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/pbuilderrc_xaTA + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' gmap = debian-installer -o gmap = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' gmap = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/pbuilderrc_xaTA --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b2 --logfile b2/build.log gmap_2024-11-20+ds-2.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Sep 19 04:59:00 +14 2025 I: pbuilder-time-stamp: 1758207540 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gmap_2024-11-20+ds-2.dsc] I: copying [./gmap_2024-11-20+ds.orig.tar.xz] I: copying [./gmap_2024-11-20+ds-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gmap_2024-11-20+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting gmap in gmap-2024-11-20+ds dpkg-source: info: unpacking gmap_2024-11-20+ds.orig.tar.xz dpkg-source: info: unpacking gmap_2024-11-20+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying install-data-local dpkg-source: info: applying remove_getopt_code_copy.patch dpkg-source: info: applying simd_fixes dpkg-source: info: applying c23.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/301612/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 18 14:59 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/301612/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/301612/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DIRSTACK=() DISTRIBUTION=forky EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=879b9d08eb174724a59d21b116af9e25 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=301612 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/pbuilderrc_xaTA --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b2 --logfile b2/build.log gmap_2024-11-20+ds-2.dsc' SUDO_GID=110 SUDO_HOME=/var/lib/jenkins SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/301612/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), architecture-is-little-endian, help2man, libbz2-dev, zlib1g-dev, debhelper, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 12.9 MB of archives. After unpacking 53.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get: 13 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 24 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 help2man amd64 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 12.9 MB in 1s (12.7 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package architecture-properties:amd64. Preparing to unpack .../11-architecture-properties_0.2.6_amd64.deb ... Unpacking architecture-properties:amd64 (0.2.6) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../23-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../25-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../26-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package help2man. Preparing to unpack .../31-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../32-libbz2-dev_1.0.8-6_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-6) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../33-libsimde-dev_0.8.2-3_all.deb ... Unpacking libsimde-dev (0.8.2-3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../34-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:amd64 (0.2.6) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/301612/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for forky I: user script /srv/workspace/pbuilder/301612/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/gmap-2024-11-20+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gmap_2024-11-20+ds-2_source.changes dpkg-buildpackage: info: source package gmap dpkg-buildpackage: info: source version 2024-11-20+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --builddir build debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_clean --builddir build_avx512 dh_auto_clean --builddir build_avx2 dh_auto_clean --builddir build_sse42 dh_auto_clean --builddir build_sse41 dh_auto_clean --builddir build_ssse3 dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_autoreconf_clean -O--builddir=build dh_clean -O--builddir=build debian/rules binary dh binary --builddir build dh_update_autotools_config -O--builddir=build dh_autoreconf -O--builddir=build configure.ac:104: installing 'config/compile' configure.ac:85: installing 'config/config.guess' configure.ac:85: installing 'config/config.sub' configure.ac:109: installing 'config/install-sh' configure.ac:109: installing 'config/missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing 'config/depcomp' src/Makefile.am:870: warning: variable 'dist_compare2truth_SOURCES' is defined but no program or src/Makefile.am:870: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1216: warning: variable 'dist_gcount_bulk_SOURCES' is defined but no program or src/Makefile.am:1216: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1242: warning: variable 'dist_gcount_sc_SOURCES' is defined but no program or src/Makefile.am:1242: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:216: warning: variable 'dist_gexact_SOURCES' is defined but no program or src/Makefile.am:216: library has 'gexact' as canonical name (possible typo) src/Makefile.am:742: warning: variable 'dist_gexact_arm_SOURCES' is defined but no program or src/Makefile.am:742: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:772: warning: variable 'dist_gexact_avx2_SOURCES' is defined but no program or src/Makefile.am:772: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:778: warning: variable 'dist_gexact_avx512_SOURCES' is defined but no program or src/Makefile.am:778: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:784: warning: variable 'dist_gexact_avx512bw_SOURCES' is defined but no program or src/Makefile.am:784: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:736: warning: variable 'dist_gexact_nosimd_SOURCES' is defined but no program or src/Makefile.am:736: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:748: warning: variable 'dist_gexact_sse2_SOURCES' is defined but no program or src/Makefile.am:748: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:760: warning: variable 'dist_gexact_sse41_SOURCES' is defined but no program or src/Makefile.am:760: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:766: warning: variable 'dist_gexact_sse42_SOURCES' is defined but no program or src/Makefile.am:766: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:754: warning: variable 'dist_gexact_ssse3_SOURCES' is defined but no program or src/Makefile.am:754: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:223: warning: variable 'dist_gfilter_SOURCES' is defined but no program or src/Makefile.am:223: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:816: warning: variable 'dist_gfilter_arm_SOURCES' is defined but no program or src/Makefile.am:816: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:846: warning: variable 'dist_gfilter_avx2_SOURCES' is defined but no program or src/Makefile.am:846: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:852: warning: variable 'dist_gfilter_avx512_SOURCES' is defined but no program or src/Makefile.am:852: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:858: warning: variable 'dist_gfilter_avx512bw_SOURCES' is defined but no program or src/Makefile.am:858: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:810: warning: variable 'dist_gfilter_nosimd_SOURCES' is defined but no program or src/Makefile.am:810: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:822: warning: variable 'dist_gfilter_sse2_SOURCES' is defined but no program or src/Makefile.am:822: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:834: warning: variable 'dist_gfilter_sse41_SOURCES' is defined but no program or src/Makefile.am:834: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:840: warning: variable 'dist_gfilter_sse42_SOURCES' is defined but no program or src/Makefile.am:840: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:828: warning: variable 'dist_gfilter_ssse3_SOURCES' is defined but no program or src/Makefile.am:828: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1132: warning: variable 'dist_iit_pileup_SOURCES' is defined but no program or src/Makefile.am:1132: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1154: warning: variable 'dist_sam_sort_SOURCES' is defined but no program or src/Makefile.am:1154: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1172: warning: variable 'dist_umi_correct_SOURCES' is defined but no program or src/Makefile.am:1172: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1191: warning: variable 'dist_velocity_counts_SOURCES' is defined but no program or src/Makefile.am:1191: library has 'velocity_counts' as canonical name (possible typo) src/Makefile.am:869: warning: variable 'compare2truth_LDADD' is defined but no program or src/Makefile.am:869: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1215: warning: variable 'gcount_bulk_LDADD' is defined but no program or src/Makefile.am:1215: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1241: warning: variable 'gcount_sc_LDADD' is defined but no program or src/Makefile.am:1241: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:215: warning: variable 'gexact_LDADD' is defined but no program or src/Makefile.am:215: library has 'gexact' as canonical name (possible typo) src/Makefile.am:741: warning: variable 'gexact_arm_LDADD' is defined but no program or src/Makefile.am:741: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:771: warning: variable 'gexact_avx2_LDADD' is defined but no program or src/Makefile.am:771: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:777: warning: variable 'gexact_avx512_LDADD' is defined but no program or src/Makefile.am:777: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:783: warning: variable 'gexact_avx512bw_LDADD' is defined but no program or src/Makefile.am:783: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:735: warning: variable 'gexact_nosimd_LDADD' is defined but no program or src/Makefile.am:735: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:747: warning: variable 'gexact_sse2_LDADD' is defined but no program or src/Makefile.am:747: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:759: warning: variable 'gexact_sse41_LDADD' is defined but no program or src/Makefile.am:759: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:765: warning: variable 'gexact_sse42_LDADD' is defined but no program or src/Makefile.am:765: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:753: warning: variable 'gexact_ssse3_LDADD' is defined but no program or src/Makefile.am:753: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:222: warning: variable 'gfilter_LDADD' is defined but no program or src/Makefile.am:222: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:815: warning: variable 'gfilter_arm_LDADD' is defined but no program or src/Makefile.am:815: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:845: warning: variable 'gfilter_avx2_LDADD' is defined but no program or src/Makefile.am:845: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:851: warning: variable 'gfilter_avx512_LDADD' is defined but no program or src/Makefile.am:851: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:857: warning: variable 'gfilter_avx512bw_LDADD' is defined but no program or src/Makefile.am:857: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:809: warning: variable 'gfilter_nosimd_LDADD' is defined but no program or src/Makefile.am:809: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:821: warning: variable 'gfilter_sse2_LDADD' is defined but no program or src/Makefile.am:821: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:833: warning: variable 'gfilter_sse41_LDADD' is defined but no program or src/Makefile.am:833: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:839: warning: variable 'gfilter_sse42_LDADD' is defined but no program or src/Makefile.am:839: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:827: warning: variable 'gfilter_ssse3_LDADD' is defined but no program or src/Makefile.am:827: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1131: warning: variable 'iit_pileup_LDADD' is defined but no program or src/Makefile.am:1131: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1153: warning: variable 'sam_sort_LDADD' is defined but no program or src/Makefile.am:1153: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1171: warning: variable 'umi_correct_LDADD' is defined but no program or src/Makefile.am:1171: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1190: warning: variable 'velocity_counts_LDADD' is defined but no program or src/Makefile.am:1190: library has 'velocity_counts' as canonical name (possible typo) src/Makefile.am:868: warning: variable 'compare2truth_LDFLAGS' is defined but no program or src/Makefile.am:868: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1214: warning: variable 'gcount_bulk_LDFLAGS' is defined but no program or src/Makefile.am:1214: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1240: warning: variable 'gcount_sc_LDFLAGS' is defined but no program or src/Makefile.am:1240: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:214: warning: variable 'gexact_LDFLAGS' is defined but no program or src/Makefile.am:214: library has 'gexact' as canonical name (possible typo) src/Makefile.am:740: warning: variable 'gexact_arm_LDFLAGS' is defined but no program or src/Makefile.am:740: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:770: warning: variable 'gexact_avx2_LDFLAGS' is defined but no program or src/Makefile.am:770: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:776: warning: variable 'gexact_avx512_LDFLAGS' is defined but no program or src/Makefile.am:776: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:782: warning: variable 'gexact_avx512bw_LDFLAGS' is defined but no program or src/Makefile.am:782: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:734: warning: variable 'gexact_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:734: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:746: warning: variable 'gexact_sse2_LDFLAGS' is defined but no program or src/Makefile.am:746: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:758: warning: variable 'gexact_sse41_LDFLAGS' is defined but no program or src/Makefile.am:758: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:764: warning: variable 'gexact_sse42_LDFLAGS' is defined but no program or src/Makefile.am:764: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:752: warning: variable 'gexact_ssse3_LDFLAGS' is defined but no program or src/Makefile.am:752: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:221: warning: variable 'gfilter_LDFLAGS' is defined but no program or src/Makefile.am:221: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:814: warning: variable 'gfilter_arm_LDFLAGS' is defined but no program or src/Makefile.am:814: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:844: warning: variable 'gfilter_avx2_LDFLAGS' is defined but no program or src/Makefile.am:844: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:850: warning: variable 'gfilter_avx512_LDFLAGS' is defined but no program or src/Makefile.am:850: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:856: warning: variable 'gfilter_avx512bw_LDFLAGS' is defined but no program or src/Makefile.am:856: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:808: warning: variable 'gfilter_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:808: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:820: warning: variable 'gfilter_sse2_LDFLAGS' is defined but no program or src/Makefile.am:820: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:832: warning: variable 'gfilter_sse41_LDFLAGS' is defined but no program or src/Makefile.am:832: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:838: warning: variable 'gfilter_sse42_LDFLAGS' is defined but no program or src/Makefile.am:838: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:826: warning: variable 'gfilter_ssse3_LDFLAGS' is defined but no program or src/Makefile.am:826: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1130: warning: variable 'iit_pileup_LDFLAGS' is defined but no program or src/Makefile.am:1130: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1152: warning: variable 'sam_sort_LDFLAGS' is defined but no program or src/Makefile.am:1152: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1170: warning: variable 'umi_correct_LDFLAGS' is defined but no program or src/Makefile.am:1170: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1189: warning: variable 'velocity_counts_LDFLAGS' is defined but no program or src/Makefile.am:1189: library has 'velocity_counts' as canonical name (possible typo) parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' rm -Rf src/simde DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI" dh_auto_configure --reload-all-buildenv-variables -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2 cd build && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2 checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse2 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse2 checking SSE2 compiler flags to be used... -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI" dh_auto_configure --reload-all-buildenv-variables --builddir build_ssse3 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=ssse3 ax_cv_cpu_has_ssse3_ext=yes ax_cv_compile_ssse3_ext=yes ax_cv_link_tmmintrin_h=yes cd build_ssse3 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=ssse3 ax_cv_cpu_has_ssse3_ext=yes ax_cv_compile_ssse3_ext=yes ax_cv_link_tmmintrin_h=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... ssse3 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... ssse3 checking SSSE3 compiler flags to be used... -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_STTNI" dh_auto_configure --builddir build_sse41 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse41 ax_cv_cpu_has_sse41_ext=yes ax_cv_compile_sse41_ext=yes ax_cv_link_smmintrin_h=yes cd build_sse41 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse41 ax_cv_cpu_has_sse41_ext=yes ax_cv_compile_sse41_ext=yes ax_cv_link_smmintrin_h=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse41 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse41 checking SSE4.1 compiler flags to be used... -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 dh_auto_configure --builddir build_sse42 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse42 ax_cv_cpu_has_sse42_ext=yes ax_cv_compile_sse42_ext=yes ax_cv_link_nmmintrin_h=yes ax_cv_cpu_has_popcnt_ext=yes ax_make_sse42=yes ax_cv_cpu_has_bmi1_ext=yes ax_cv_compile_bmi_ext=yes ax_cv_link_bmi=yes cd build_sse42 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse42 ax_cv_cpu_has_sse42_ext=yes ax_cv_compile_sse42_ext=yes ax_cv_link_nmmintrin_h=yes ax_cv_cpu_has_popcnt_ext=yes ax_make_sse42=yes ax_cv_cpu_has_bmi1_ext=yes ax_cv_compile_bmi_ext=yes ax_cv_link_bmi=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm... yes checking for abm linker support... yes checking for _popcnt32 run support... yes checking for _lzcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi... yes checking for bmi linker support... yes checking for _tzcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse42 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse42 checking SSE4.2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 dh_auto_configure --builddir build_avx2 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx2 ax_make_avx2=yes ax_cv_cpu_has_bmi2_ext=yes ax_cv_compile_bmi2_ext=yes ax_cv_link_bmi2=yes cd build_avx2 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx2 ax_make_avx2=yes ax_cv_cpu_has_bmi2_ext=yes ax_cv_compile_bmi2_ext=yes ax_cv_link_bmi2=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2... yes checking for bmi2 linker support... yes checking for _pext run support... yes checking for user-selected SIMD level... avx2 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... avx2 checking AVX2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 dh_auto_configure --builddir build_avx512 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx512 ax_cv_cpu_has_avx512_ext=yes ax_cv_compile_avx512_ext=yes ax_cv_compile_avx512bw_ext=no ax_cv_link_avx512bw=no cd build_avx512 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx512 ax_cv_cpu_has_avx512_ext=yes ax_cv_compile_avx512_ext=yes ax_cv_compile_avx512bw_ext=no ax_cv_link_avx512bw=no checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd... yes checking for nmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw... yes checking for avx512vl and avx512bw linker support... yes checking for user-selected SIMD level... avx512 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... avx512 checking AVX512 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw # skipping avx512bw for now: # ../../src/oligoindex_hr.c: In function 'count_positions_fwd_simd': make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_build cd build && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/compress-write.c: In function 'Compress_compress': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/iit-read.c: In function 'IIT_read': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/compress-write.c: In function 'put_compressed_one': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.sse2 gmap_sse2-except.o gmap_sse2-assert.o gmap_sse2-mem.o gmap_sse2-intlist.o gmap_sse2-uintlist.o gmap_sse2-list.o gmap_sse2-littleendian.o gmap_sse2-bigendian.o gmap_sse2-univinterval.o gmap_sse2-interval.o gmap_sse2-stopwatch.o gmap_sse2-semaphore.o gmap_sse2-access.o gmap_sse2-filestring.o gmap_sse2-iit-read-univ.o gmap_sse2-iit-read.o gmap_sse2-md5.o gmap_sse2-bzip2.o gmap_sse2-fopen.o gmap_sse2-sequence.o gmap_sse2-reader.o gmap_sse2-genomicpos.o gmap_sse2-compress.o gmap_sse2-compress-write.o gmap_sse2-gbuffer.o gmap_sse2-genome.o gmap_sse2-popcount.o gmap_sse2-dinucl_bits.o gmap_sse2-genome_canonical.o gmap_sse2-genome-write.o gmap_sse2-bitpack64-read.o gmap_sse2-bitpack64-readtwo.o gmap_sse2-indexdb.o gmap_sse2-oligo.o gmap_sse2-block.o gmap_sse2-chrom.o gmap_sse2-segmentpos.o gmap_sse2-chrnum.o gmap_sse2-uinttable_rh.o gmap_sse2-gregion.o gmap_sse2-match.o gmap_sse2-matchpool.o gmap_sse2-diagnostic.o gmap_sse2-stage1.o gmap_sse2-diag.o gmap_sse2-diagpool.o gmap_sse2-cmet.o gmap_sse2-atoi.o gmap_sse2-orderstat.o gmap_sse2-oligoindex_hr.o gmap_sse2-intron.o gmap_sse2-maxent.o gmap_sse2-maxent_hr.o gmap_sse2-pair.o gmap_sse2-pairpool.o gmap_sse2-cellpool.o gmap_sse2-stage2.o gmap_sse2-doublelist.o gmap_sse2-smooth.o gmap_sse2-splicestringpool.o gmap_sse2-splicetrie_build.o gmap_sse2-splicetrie.o gmap_sse2-boyer-moore.o gmap_sse2-dynprog.o gmap_sse2-dynprog_simd.o gmap_sse2-dynprog_single.o gmap_sse2-dynprog_genome.o gmap_sse2-dynprog_cdna.o gmap_sse2-dynprog_end.o gmap_sse2-translation.o gmap_sse2-pbinom.o gmap_sse2-changepoint.o gmap_sse2-stage3.o gmap_sse2-request.o gmap_sse2-result.o gmap_sse2-output.o gmap_sse2-inbuffer.o gmap_sse2-samheader.o gmap_sse2-printbuffer.o gmap_sse2-outbuffer.o gmap_sse2-chimera.o gmap_sse2-datadir.o gmap_sse2-parserange.o gmap_sse2-getline.o gmap_sse2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.sse2 gsnap_sse2-except.o gsnap_sse2-assert.o gsnap_sse2-mem.o gsnap_sse2-intlist.o gsnap_sse2-uintlist.o gsnap_sse2-list.o gsnap_sse2-littleendian.o gsnap_sse2-bigendian.o gsnap_sse2-univinterval.o gsnap_sse2-interval.o gsnap_sse2-stopwatch.o gsnap_sse2-semaphore.o gsnap_sse2-access.o gsnap_sse2-filestring.o gsnap_sse2-iit-read-univ.o gsnap_sse2-iit-read.o gsnap_sse2-bzip2.o gsnap_sse2-reader.o gsnap_sse2-genomicpos.o gsnap_sse2-compress.o gsnap_sse2-genome.o gsnap_sse2-transcriptome.o gsnap_sse2-popcount.o gsnap_sse2-genomebits.o gsnap_sse2-genomebits_consec.o gsnap_sse2-genomebits_count.o gsnap_sse2-genomebits_kmer.o gsnap_sse2-genomebits_indel.o gsnap_sse2-genomebits_decode.o gsnap_sse2-genomebits_mismatches.o gsnap_sse2-genomebits_trim.o gsnap_sse2-dinucl_bits.o gsnap_sse2-genome_sites.o gsnap_sse2-bitpack64-read.o gsnap_sse2-bitpack64-readtwo.o gsnap_sse2-mergeinfo.o gsnap_sse2-merge-diagonals-heap-uint4.o gsnap_sse2-merge-uint4.o gsnap_sse2-merge-diagonals-simd-uint4.o gsnap_sse2-indexdb.o gsnap_sse2-localdb-read.o gsnap_sse2-oligo.o gsnap_sse2-chrnum.o gsnap_sse2-maxent_hr.o gsnap_sse2-mapq.o gsnap_sse2-fopen.o gsnap_sse2-shortread.o gsnap_sse2-junction.o gsnap_sse2-concordance.o gsnap_sse2-simplepair.o gsnap_sse2-orderstat.o gsnap_sse2-intlistpool.o gsnap_sse2-uintlistpool.o gsnap_sse2-listpool.o gsnap_sse2-hitlistpool.o gsnap_sse2-pathpool.o gsnap_sse2-auxinfopool.o gsnap_sse2-pathstorepool.o gsnap_sse2-intron.o gsnap_sse2-gbuffer.o gsnap_sse2-select64-common.o gsnap_sse2-select64-ones.o gsnap_sse2-select64-zeroes.o gsnap_sse2-ef64.o gsnap_sse2-nr-x.o gsnap_sse2-knownsplicing.o gsnap_sse2-knownindels.o gsnap_sse2-splice.o gsnap_sse2-indel.o gsnap_sse2-spliceendsgen.o gsnap_sse2-spliceends.o gsnap_sse2-bitpack64-access.o gsnap_sse2-trdiag.o gsnap_sse2-trdiagpool.o gsnap_sse2-tr-extension-search.o gsnap_sse2-univdiag.o gsnap_sse2-univdiagpool.o gsnap_sse2-sedgesort.o gsnap_sse2-auxinfo.o gsnap_sse2-pathstore.o gsnap_sse2-altsplice.o gsnap_sse2-path.o gsnap_sse2-pathpair.o gsnap_sse2-path-solve.o gsnap_sse2-path-fusion.o gsnap_sse2-path-trim.o gsnap_sse2-path-eval.o gsnap_sse2-pathpair-eval.o gsnap_sse2-path-print-alignment.o gsnap_sse2-path-print-m8.o gsnap_sse2-path-print-sam.o gsnap_sse2-path-learn.o gsnap_sse2-method.o gsnap_sse2-doublelist.o gsnap_sse2-bitvector.o gsnap_sse2-transcriptpool.o gsnap_sse2-exon.o gsnap_sse2-transcript.o gsnap_sse2-trpathpool.o gsnap_sse2-trpath.o gsnap_sse2-trpath-solve.o gsnap_sse2-trpath-convert.o gsnap_sse2-trpath-eval.o gsnap_sse2-transcriptome-search.o gsnap_sse2-vectorpool.o gsnap_sse2-repair.o gsnap_sse2-transcript-remap.o gsnap_sse2-transcript-velocity.o gsnap_sse2-intersect-small.o gsnap_sse2-intersect-uint2.o gsnap_sse2-intersect-approx-uint4.o gsnap_sse2-intersect-approx-indices-uint4.o gsnap_sse2-intersect-wdups-indices.o gsnap_sse2-intersect-lower-small.o gsnap_sse2-intersect-higher-small.o gsnap_sse2-intersect-indices-small.o gsnap_sse2-intersect-indices2-small.o gsnap_sse2-intersect-concordance-uint4.o gsnap_sse2-kmer-search.o gsnap_sse2-extension-search.o gsnap_sse2-repetitive.o gsnap_sse2-uint8table.o gsnap_sse2-uinttable.o gsnap_sse2-stage1hr.o gsnap_sse2-stage1hr-single.o gsnap_sse2-stage1hr-paired.o gsnap_sse2-uinttableuint.o gsnap_sse2-tableuint.o gsnap_sse2-single-cell.o gsnap_sse2-request.o gsnap_sse2-resulthr.o gsnap_sse2-output.o gsnap_sse2-inbuffer.o gsnap_sse2-samheader.o gsnap_sse2-printbuffer.o gsnap_sse2-outbuffer.o gsnap_sse2-uintpairtable.o gsnap_sse2-splice-count.o gsnap_sse2-support.o gsnap_sse2-datadir.o gsnap_sse2-parserange.o gsnap_sse2-getline.o gsnap_sse2-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.sse2 gmapl_sse2-except.o gmapl_sse2-assert.o gmapl_sse2-mem.o gmapl_sse2-intlist.o gmapl_sse2-uintlist.o gmapl_sse2-uint8list.o gmapl_sse2-list.o gmapl_sse2-littleendian.o gmapl_sse2-bigendian.o gmapl_sse2-univinterval.o gmapl_sse2-interval.o gmapl_sse2-stopwatch.o gmapl_sse2-semaphore.o gmapl_sse2-access.o gmapl_sse2-filestring.o gmapl_sse2-iit-read-univ.o gmapl_sse2-iit-read.o gmapl_sse2-md5.o gmapl_sse2-bzip2.o gmapl_sse2-fopen.o gmapl_sse2-sequence.o gmapl_sse2-reader.o gmapl_sse2-genomicpos.o gmapl_sse2-compress.o gmapl_sse2-compress-write.o gmapl_sse2-gbuffer.o gmapl_sse2-genome.o gmapl_sse2-popcount.o gmapl_sse2-dinucl_bits.o gmapl_sse2-genome_canonical.o gmapl_sse2-genome-write.o gmapl_sse2-bitpack64-read.o gmapl_sse2-bitpack64-readtwo.o gmapl_sse2-indexdb.o gmapl_sse2-oligo.o gmapl_sse2-block.o gmapl_sse2-chrom.o gmapl_sse2-segmentpos.o gmapl_sse2-chrnum.o gmapl_sse2-uinttable_rh.o gmapl_sse2-uint8table_rh.o gmapl_sse2-gregion.o gmapl_sse2-match.o gmapl_sse2-matchpool.o gmapl_sse2-diagnostic.o gmapl_sse2-stage1.o gmapl_sse2-diag.o gmapl_sse2-diagpool.o gmapl_sse2-cmet.o gmapl_sse2-atoi.o gmapl_sse2-orderstat.o gmapl_sse2-oligoindex_hr.o gmapl_sse2-intron.o gmapl_sse2-maxent.o gmapl_sse2-maxent_hr.o gmapl_sse2-pair.o gmapl_sse2-pairpool.o gmapl_sse2-cellpool.o gmapl_sse2-stage2.o gmapl_sse2-doublelist.o gmapl_sse2-smooth.o gmapl_sse2-splicestringpool.o gmapl_sse2-splicetrie_build.o gmapl_sse2-splicetrie.o gmapl_sse2-boyer-moore.o gmapl_sse2-dynprog.o gmapl_sse2-dynprog_simd.o gmapl_sse2-dynprog_single.o gmapl_sse2-dynprog_genome.o gmapl_sse2-dynprog_cdna.o gmapl_sse2-dynprog_end.o gmapl_sse2-translation.o gmapl_sse2-pbinom.o gmapl_sse2-changepoint.o gmapl_sse2-stage3.o gmapl_sse2-request.o gmapl_sse2-result.o gmapl_sse2-output.o gmapl_sse2-inbuffer.o gmapl_sse2-samheader.o gmapl_sse2-printbuffer.o gmapl_sse2-outbuffer.o gmapl_sse2-chimera.o gmapl_sse2-datadir.o gmapl_sse2-parserange.o gmapl_sse2-getline.o gmapl_sse2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.sse2 gsnapl_sse2-except.o gsnapl_sse2-assert.o gsnapl_sse2-mem.o gsnapl_sse2-intlist.o gsnapl_sse2-uintlist.o gsnapl_sse2-uint8list.o gsnapl_sse2-list.o gsnapl_sse2-littleendian.o gsnapl_sse2-bigendian.o gsnapl_sse2-univinterval.o gsnapl_sse2-interval.o gsnapl_sse2-stopwatch.o gsnapl_sse2-semaphore.o gsnapl_sse2-access.o gsnapl_sse2-filestring.o gsnapl_sse2-iit-read-univ.o gsnapl_sse2-iit-read.o gsnapl_sse2-bzip2.o gsnapl_sse2-reader.o gsnapl_sse2-genomicpos.o gsnapl_sse2-compress.o gsnapl_sse2-genome.o gsnapl_sse2-transcriptome.o gsnapl_sse2-popcount.o gsnapl_sse2-genomebits.o gsnapl_sse2-genomebits_consec.o gsnapl_sse2-genomebits_count.o gsnapl_sse2-genomebits_kmer.o gsnapl_sse2-genomebits_indel.o gsnapl_sse2-genomebits_decode.o gsnapl_sse2-genomebits_mismatches.o gsnapl_sse2-genomebits_trim.o gsnapl_sse2-dinucl_bits.o gsnapl_sse2-genome_sites.o gsnapl_sse2-bitpack64-read.o gsnapl_sse2-bitpack64-readtwo.o gsnapl_sse2-mergeinfo.o gsnapl_sse2-merge-diagonals-heap-uint8.o gsnapl_sse2-merge-uint8.o gsnapl_sse2-merge-diagonals-simd-uint8.o gsnapl_sse2-merge-diagonals-heap-uint4.o gsnapl_sse2-merge-uint4.o gsnapl_sse2-merge-diagonals-simd-uint4.o gsnapl_sse2-indexdb.o gsnapl_sse2-localdb-read.o gsnapl_sse2-oligo.o gsnapl_sse2-chrnum.o gsnapl_sse2-maxent_hr.o gsnapl_sse2-mapq.o gsnapl_sse2-fopen.o gsnapl_sse2-shortread.o gsnapl_sse2-junction.o gsnapl_sse2-concordance.o gsnapl_sse2-simplepair.o gsnapl_sse2-orderstat.o gsnapl_sse2-intlistpool.o gsnapl_sse2-uintlistpool.o gsnapl_sse2-uint8listpool.o gsnapl_sse2-listpool.o gsnapl_sse2-hitlistpool.o gsnapl_sse2-pathpool.o gsnapl_sse2-auxinfopool.o gsnapl_sse2-pathstorepool.o gsnapl_sse2-intron.o gsnapl_sse2-gbuffer.o gsnapl_sse2-select64-common.o gsnapl_sse2-select64-ones.o gsnapl_sse2-select64-zeroes.o gsnapl_sse2-ef64.o gsnapl_sse2-nr-x.o gsnapl_sse2-knownsplicing.o gsnapl_sse2-knownindels.o gsnapl_sse2-splice.o gsnapl_sse2-indel.o gsnapl_sse2-spliceendsgen.o gsnapl_sse2-spliceends.o gsnapl_sse2-bitpack64-access.o gsnapl_sse2-trdiag.o gsnapl_sse2-trdiagpool.o gsnapl_sse2-tr-extension-search.o gsnapl_sse2-univdiag.o gsnapl_sse2-univdiagpool.o gsnapl_sse2-sedgesort.o gsnapl_sse2-auxinfo.o gsnapl_sse2-pathstore.o gsnapl_sse2-altsplice.o gsnapl_sse2-path.o gsnapl_sse2-pathpair.o gsnapl_sse2-path-solve.o gsnapl_sse2-path-fusion.o gsnapl_sse2-path-trim.o gsnapl_sse2-path-eval.o gsnapl_sse2-pathpair-eval.o gsnapl_sse2-path-print-alignment.o gsnapl_sse2-path-print-m8.o gsnapl_sse2-path-print-sam.o gsnapl_sse2-path-learn.o gsnapl_sse2-method.o gsnapl_sse2-doublelist.o gsnapl_sse2-bitvector.o gsnapl_sse2-transcriptpool.o gsnapl_sse2-exon.o gsnapl_sse2-transcript.o gsnapl_sse2-trpathpool.o gsnapl_sse2-trpath.o gsnapl_sse2-trpath-solve.o gsnapl_sse2-trpath-convert.o gsnapl_sse2-trpath-eval.o gsnapl_sse2-transcriptome-search.o gsnapl_sse2-vectorpool.o gsnapl_sse2-repair.o gsnapl_sse2-transcript-remap.o gsnapl_sse2-transcript-velocity.o gsnapl_sse2-intersect-large.o gsnapl_sse2-intersect-small.o gsnapl_sse2-intersect-uint2.o gsnapl_sse2-intersect-approx-uint4.o gsnapl_sse2-intersect-approx-uint8.o gsnapl_sse2-intersect-approx-indices-uint8.o gsnapl_sse2-intersect-wdups-indices.o gsnapl_sse2-intersect-lower-large.o gsnapl_sse2-intersect-higher-large.o gsnapl_sse2-intersect-indices-small.o gsnapl_sse2-intersect-indices2-large.o gsnapl_sse2-intersect-indices-uint8.o gsnapl_sse2-intersect-concordance-uint8.o gsnapl_sse2-kmer-search.o gsnapl_sse2-extension-search.o gsnapl_sse2-repetitive.o gsnapl_sse2-uint8table.o gsnapl_sse2-stage1hr.o gsnapl_sse2-stage1hr-single.o gsnapl_sse2-stage1hr-paired.o gsnapl_sse2-uint8tableuint.o gsnapl_sse2-tableuint.o gsnapl_sse2-single-cell.o gsnapl_sse2-request.o gsnapl_sse2-resulthr.o gsnapl_sse2-output.o gsnapl_sse2-inbuffer.o gsnapl_sse2-samheader.o gsnapl_sse2-printbuffer.o gsnapl_sse2-outbuffer.o gsnapl_sse2-uint8pairtable.o gsnapl_sse2-splice-count.o gsnapl_sse2-support.o gsnapl_sse2-datadir.o gsnapl_sse2-parserange.o gsnapl_sse2-getline.o gsnapl_sse2-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords chmod +x md_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x psl_splicesites chmod +x psl_introns chmod +x psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x ensembl_genes cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites cp gtf_genes.pl gtf_genes chmod +x gtf_introns chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gtf_transcript_splicesites cp gff3_genes.pl gff3_genes chmod +x gff3_introns chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x dbsnp_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' dh_auto_build --builddir build_ssse3 cd build_ssse3 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb.c: In function 'positions_read_multiple': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple_large': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.ssse3 gmap_ssse3-except.o gmap_ssse3-assert.o gmap_ssse3-mem.o gmap_ssse3-intlist.o gmap_ssse3-uintlist.o gmap_ssse3-list.o gmap_ssse3-littleendian.o gmap_ssse3-bigendian.o gmap_ssse3-univinterval.o gmap_ssse3-interval.o gmap_ssse3-stopwatch.o gmap_ssse3-semaphore.o gmap_ssse3-access.o gmap_ssse3-filestring.o gmap_ssse3-iit-read-univ.o gmap_ssse3-iit-read.o gmap_ssse3-md5.o gmap_ssse3-bzip2.o gmap_ssse3-fopen.o gmap_ssse3-sequence.o gmap_ssse3-reader.o gmap_ssse3-genomicpos.o gmap_ssse3-compress.o gmap_ssse3-compress-write.o gmap_ssse3-gbuffer.o gmap_ssse3-genome.o gmap_ssse3-popcount.o gmap_ssse3-dinucl_bits.o gmap_ssse3-genome_canonical.o gmap_ssse3-genome-write.o gmap_ssse3-bitpack64-read.o gmap_ssse3-bitpack64-readtwo.o gmap_ssse3-indexdb.o gmap_ssse3-oligo.o gmap_ssse3-block.o gmap_ssse3-chrom.o gmap_ssse3-segmentpos.o gmap_ssse3-chrnum.o gmap_ssse3-uinttable_rh.o gmap_ssse3-gregion.o gmap_ssse3-match.o gmap_ssse3-matchpool.o gmap_ssse3-diagnostic.o gmap_ssse3-stage1.o gmap_ssse3-diag.o gmap_ssse3-diagpool.o gmap_ssse3-cmet.o gmap_ssse3-atoi.o gmap_ssse3-orderstat.o gmap_ssse3-oligoindex_hr.o gmap_ssse3-intron.o gmap_ssse3-maxent.o gmap_ssse3-maxent_hr.o gmap_ssse3-pair.o gmap_ssse3-pairpool.o gmap_ssse3-cellpool.o gmap_ssse3-stage2.o gmap_ssse3-doublelist.o gmap_ssse3-smooth.o gmap_ssse3-splicestringpool.o gmap_ssse3-splicetrie_build.o gmap_ssse3-splicetrie.o gmap_ssse3-boyer-moore.o gmap_ssse3-dynprog.o gmap_ssse3-dynprog_simd.o gmap_ssse3-dynprog_single.o gmap_ssse3-dynprog_genome.o gmap_ssse3-dynprog_cdna.o gmap_ssse3-dynprog_end.o gmap_ssse3-translation.o gmap_ssse3-pbinom.o gmap_ssse3-changepoint.o gmap_ssse3-stage3.o gmap_ssse3-request.o gmap_ssse3-result.o gmap_ssse3-output.o gmap_ssse3-inbuffer.o gmap_ssse3-samheader.o gmap_ssse3-printbuffer.o gmap_ssse3-outbuffer.o gmap_ssse3-chimera.o gmap_ssse3-datadir.o gmap_ssse3-parserange.o gmap_ssse3-getline.o gmap_ssse3-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.ssse3 gsnap_ssse3-except.o gsnap_ssse3-assert.o gsnap_ssse3-mem.o gsnap_ssse3-intlist.o gsnap_ssse3-uintlist.o gsnap_ssse3-list.o gsnap_ssse3-littleendian.o gsnap_ssse3-bigendian.o gsnap_ssse3-univinterval.o gsnap_ssse3-interval.o gsnap_ssse3-stopwatch.o gsnap_ssse3-semaphore.o gsnap_ssse3-access.o gsnap_ssse3-filestring.o gsnap_ssse3-iit-read-univ.o gsnap_ssse3-iit-read.o gsnap_ssse3-bzip2.o gsnap_ssse3-reader.o gsnap_ssse3-genomicpos.o gsnap_ssse3-compress.o gsnap_ssse3-genome.o gsnap_ssse3-transcriptome.o gsnap_ssse3-popcount.o gsnap_ssse3-genomebits.o gsnap_ssse3-genomebits_consec.o gsnap_ssse3-genomebits_count.o gsnap_ssse3-genomebits_kmer.o gsnap_ssse3-genomebits_indel.o gsnap_ssse3-genomebits_decode.o gsnap_ssse3-genomebits_mismatches.o gsnap_ssse3-genomebits_trim.o gsnap_ssse3-dinucl_bits.o gsnap_ssse3-genome_sites.o gsnap_ssse3-bitpack64-read.o gsnap_ssse3-bitpack64-readtwo.o gsnap_ssse3-mergeinfo.o gsnap_ssse3-merge-diagonals-heap-uint4.o gsnap_ssse3-merge-uint4.o gsnap_ssse3-merge-diagonals-simd-uint4.o gsnap_ssse3-indexdb.o gsnap_ssse3-localdb-read.o gsnap_ssse3-oligo.o gsnap_ssse3-chrnum.o gsnap_ssse3-maxent_hr.o gsnap_ssse3-mapq.o gsnap_ssse3-fopen.o gsnap_ssse3-shortread.o gsnap_ssse3-junction.o gsnap_ssse3-concordance.o gsnap_ssse3-simplepair.o gsnap_ssse3-orderstat.o gsnap_ssse3-intlistpool.o gsnap_ssse3-uintlistpool.o gsnap_ssse3-listpool.o gsnap_ssse3-hitlistpool.o gsnap_ssse3-pathpool.o gsnap_ssse3-auxinfopool.o gsnap_ssse3-pathstorepool.o gsnap_ssse3-intron.o gsnap_ssse3-gbuffer.o gsnap_ssse3-select64-common.o gsnap_ssse3-select64-ones.o gsnap_ssse3-select64-zeroes.o gsnap_ssse3-ef64.o gsnap_ssse3-nr-x.o gsnap_ssse3-knownsplicing.o gsnap_ssse3-knownindels.o gsnap_ssse3-splice.o gsnap_ssse3-indel.o gsnap_ssse3-spliceendsgen.o gsnap_ssse3-spliceends.o gsnap_ssse3-bitpack64-access.o gsnap_ssse3-trdiag.o gsnap_ssse3-trdiagpool.o gsnap_ssse3-tr-extension-search.o gsnap_ssse3-univdiag.o gsnap_ssse3-univdiagpool.o gsnap_ssse3-sedgesort.o gsnap_ssse3-auxinfo.o gsnap_ssse3-pathstore.o gsnap_ssse3-altsplice.o gsnap_ssse3-path.o gsnap_ssse3-pathpair.o gsnap_ssse3-path-solve.o gsnap_ssse3-path-fusion.o gsnap_ssse3-path-trim.o gsnap_ssse3-path-eval.o gsnap_ssse3-pathpair-eval.o gsnap_ssse3-path-print-alignment.o gsnap_ssse3-path-print-m8.o gsnap_ssse3-path-print-sam.o gsnap_ssse3-path-learn.o gsnap_ssse3-method.o gsnap_ssse3-doublelist.o gsnap_ssse3-bitvector.o gsnap_ssse3-transcriptpool.o gsnap_ssse3-exon.o gsnap_ssse3-transcript.o gsnap_ssse3-trpathpool.o gsnap_ssse3-trpath.o gsnap_ssse3-trpath-solve.o gsnap_ssse3-trpath-convert.o gsnap_ssse3-trpath-eval.o gsnap_ssse3-transcriptome-search.o gsnap_ssse3-vectorpool.o gsnap_ssse3-repair.o gsnap_ssse3-transcript-remap.o gsnap_ssse3-transcript-velocity.o gsnap_ssse3-intersect-small.o gsnap_ssse3-intersect-uint2.o gsnap_ssse3-intersect-approx-uint4.o gsnap_ssse3-intersect-approx-indices-uint4.o gsnap_ssse3-intersect-wdups-indices.o gsnap_ssse3-intersect-lower-small.o gsnap_ssse3-intersect-higher-small.o gsnap_ssse3-intersect-indices-small.o gsnap_ssse3-intersect-indices2-small.o gsnap_ssse3-intersect-concordance-uint4.o gsnap_ssse3-kmer-search.o gsnap_ssse3-extension-search.o gsnap_ssse3-repetitive.o gsnap_ssse3-uint8table.o gsnap_ssse3-uinttable.o gsnap_ssse3-stage1hr.o gsnap_ssse3-stage1hr-single.o gsnap_ssse3-stage1hr-paired.o gsnap_ssse3-uinttableuint.o gsnap_ssse3-tableuint.o gsnap_ssse3-single-cell.o gsnap_ssse3-request.o gsnap_ssse3-resulthr.o gsnap_ssse3-output.o gsnap_ssse3-inbuffer.o gsnap_ssse3-samheader.o gsnap_ssse3-printbuffer.o gsnap_ssse3-outbuffer.o gsnap_ssse3-uintpairtable.o gsnap_ssse3-splice-count.o gsnap_ssse3-support.o gsnap_ssse3-datadir.o gsnap_ssse3-parserange.o gsnap_ssse3-getline.o gsnap_ssse3-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.ssse3 gmapl_ssse3-except.o gmapl_ssse3-assert.o gmapl_ssse3-mem.o gmapl_ssse3-intlist.o gmapl_ssse3-uintlist.o gmapl_ssse3-uint8list.o gmapl_ssse3-list.o gmapl_ssse3-littleendian.o gmapl_ssse3-bigendian.o gmapl_ssse3-univinterval.o gmapl_ssse3-interval.o gmapl_ssse3-stopwatch.o gmapl_ssse3-semaphore.o gmapl_ssse3-access.o gmapl_ssse3-filestring.o gmapl_ssse3-iit-read-univ.o gmapl_ssse3-iit-read.o gmapl_ssse3-md5.o gmapl_ssse3-bzip2.o gmapl_ssse3-fopen.o gmapl_ssse3-sequence.o gmapl_ssse3-reader.o gmapl_ssse3-genomicpos.o gmapl_ssse3-compress.o gmapl_ssse3-compress-write.o gmapl_ssse3-gbuffer.o gmapl_ssse3-genome.o gmapl_ssse3-popcount.o gmapl_ssse3-dinucl_bits.o gmapl_ssse3-genome_canonical.o gmapl_ssse3-genome-write.o gmapl_ssse3-bitpack64-read.o gmapl_ssse3-bitpack64-readtwo.o gmapl_ssse3-indexdb.o gmapl_ssse3-oligo.o gmapl_ssse3-block.o gmapl_ssse3-chrom.o gmapl_ssse3-segmentpos.o gmapl_ssse3-chrnum.o gmapl_ssse3-uinttable_rh.o gmapl_ssse3-uint8table_rh.o gmapl_ssse3-gregion.o gmapl_ssse3-match.o gmapl_ssse3-matchpool.o gmapl_ssse3-diagnostic.o gmapl_ssse3-stage1.o gmapl_ssse3-diag.o gmapl_ssse3-diagpool.o gmapl_ssse3-cmet.o gmapl_ssse3-atoi.o gmapl_ssse3-orderstat.o gmapl_ssse3-oligoindex_hr.o gmapl_ssse3-intron.o gmapl_ssse3-maxent.o gmapl_ssse3-maxent_hr.o gmapl_ssse3-pair.o gmapl_ssse3-pairpool.o gmapl_ssse3-cellpool.o gmapl_ssse3-stage2.o gmapl_ssse3-doublelist.o gmapl_ssse3-smooth.o gmapl_ssse3-splicestringpool.o gmapl_ssse3-splicetrie_build.o gmapl_ssse3-splicetrie.o gmapl_ssse3-boyer-moore.o gmapl_ssse3-dynprog.o gmapl_ssse3-dynprog_simd.o gmapl_ssse3-dynprog_single.o gmapl_ssse3-dynprog_genome.o gmapl_ssse3-dynprog_cdna.o gmapl_ssse3-dynprog_end.o gmapl_ssse3-translation.o gmapl_ssse3-pbinom.o gmapl_ssse3-changepoint.o gmapl_ssse3-stage3.o gmapl_ssse3-request.o gmapl_ssse3-result.o gmapl_ssse3-output.o gmapl_ssse3-inbuffer.o gmapl_ssse3-samheader.o gmapl_ssse3-printbuffer.o gmapl_ssse3-outbuffer.o gmapl_ssse3-chimera.o gmapl_ssse3-datadir.o gmapl_ssse3-parserange.o gmapl_ssse3-getline.o gmapl_ssse3-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.ssse3 gsnapl_ssse3-except.o gsnapl_ssse3-assert.o gsnapl_ssse3-mem.o gsnapl_ssse3-intlist.o gsnapl_ssse3-uintlist.o gsnapl_ssse3-uint8list.o gsnapl_ssse3-list.o gsnapl_ssse3-littleendian.o gsnapl_ssse3-bigendian.o gsnapl_ssse3-univinterval.o gsnapl_ssse3-interval.o gsnapl_ssse3-stopwatch.o gsnapl_ssse3-semaphore.o gsnapl_ssse3-access.o gsnapl_ssse3-filestring.o gsnapl_ssse3-iit-read-univ.o gsnapl_ssse3-iit-read.o gsnapl_ssse3-bzip2.o gsnapl_ssse3-reader.o gsnapl_ssse3-genomicpos.o gsnapl_ssse3-compress.o gsnapl_ssse3-genome.o gsnapl_ssse3-transcriptome.o gsnapl_ssse3-popcount.o gsnapl_ssse3-genomebits.o gsnapl_ssse3-genomebits_consec.o gsnapl_ssse3-genomebits_count.o gsnapl_ssse3-genomebits_kmer.o gsnapl_ssse3-genomebits_indel.o gsnapl_ssse3-genomebits_decode.o gsnapl_ssse3-genomebits_mismatches.o gsnapl_ssse3-genomebits_trim.o gsnapl_ssse3-dinucl_bits.o gsnapl_ssse3-genome_sites.o gsnapl_ssse3-bitpack64-read.o gsnapl_ssse3-bitpack64-readtwo.o gsnapl_ssse3-mergeinfo.o gsnapl_ssse3-merge-diagonals-heap-uint8.o gsnapl_ssse3-merge-uint8.o gsnapl_ssse3-merge-diagonals-simd-uint8.o gsnapl_ssse3-merge-diagonals-heap-uint4.o gsnapl_ssse3-merge-uint4.o gsnapl_ssse3-merge-diagonals-simd-uint4.o gsnapl_ssse3-indexdb.o gsnapl_ssse3-localdb-read.o gsnapl_ssse3-oligo.o gsnapl_ssse3-chrnum.o gsnapl_ssse3-maxent_hr.o gsnapl_ssse3-mapq.o gsnapl_ssse3-fopen.o gsnapl_ssse3-shortread.o gsnapl_ssse3-junction.o gsnapl_ssse3-concordance.o gsnapl_ssse3-simplepair.o gsnapl_ssse3-orderstat.o gsnapl_ssse3-intlistpool.o gsnapl_ssse3-uintlistpool.o gsnapl_ssse3-uint8listpool.o gsnapl_ssse3-listpool.o gsnapl_ssse3-hitlistpool.o gsnapl_ssse3-pathpool.o gsnapl_ssse3-auxinfopool.o gsnapl_ssse3-pathstorepool.o gsnapl_ssse3-intron.o gsnapl_ssse3-gbuffer.o gsnapl_ssse3-select64-common.o gsnapl_ssse3-select64-ones.o gsnapl_ssse3-select64-zeroes.o gsnapl_ssse3-ef64.o gsnapl_ssse3-nr-x.o gsnapl_ssse3-knownsplicing.o gsnapl_ssse3-knownindels.o gsnapl_ssse3-splice.o gsnapl_ssse3-indel.o gsnapl_ssse3-spliceendsgen.o gsnapl_ssse3-spliceends.o gsnapl_ssse3-bitpack64-access.o gsnapl_ssse3-trdiag.o gsnapl_ssse3-trdiagpool.o gsnapl_ssse3-tr-extension-search.o gsnapl_ssse3-univdiag.o gsnapl_ssse3-univdiagpool.o gsnapl_ssse3-sedgesort.o gsnapl_ssse3-auxinfo.o gsnapl_ssse3-pathstore.o gsnapl_ssse3-altsplice.o gsnapl_ssse3-path.o gsnapl_ssse3-pathpair.o gsnapl_ssse3-path-solve.o gsnapl_ssse3-path-fusion.o gsnapl_ssse3-path-trim.o gsnapl_ssse3-path-eval.o gsnapl_ssse3-pathpair-eval.o gsnapl_ssse3-path-print-alignment.o gsnapl_ssse3-path-print-m8.o gsnapl_ssse3-path-print-sam.o gsnapl_ssse3-path-learn.o gsnapl_ssse3-method.o gsnapl_ssse3-doublelist.o gsnapl_ssse3-bitvector.o gsnapl_ssse3-transcriptpool.o gsnapl_ssse3-exon.o gsnapl_ssse3-transcript.o gsnapl_ssse3-trpathpool.o gsnapl_ssse3-trpath.o gsnapl_ssse3-trpath-solve.o gsnapl_ssse3-trpath-convert.o gsnapl_ssse3-trpath-eval.o gsnapl_ssse3-transcriptome-search.o gsnapl_ssse3-vectorpool.o gsnapl_ssse3-repair.o gsnapl_ssse3-transcript-remap.o gsnapl_ssse3-transcript-velocity.o gsnapl_ssse3-intersect-large.o gsnapl_ssse3-intersect-small.o gsnapl_ssse3-intersect-uint2.o gsnapl_ssse3-intersect-approx-uint4.o gsnapl_ssse3-intersect-approx-uint8.o gsnapl_ssse3-intersect-approx-indices-uint8.o gsnapl_ssse3-intersect-wdups-indices.o gsnapl_ssse3-intersect-lower-large.o gsnapl_ssse3-intersect-higher-large.o gsnapl_ssse3-intersect-indices-small.o gsnapl_ssse3-intersect-indices2-large.o gsnapl_ssse3-intersect-indices-uint8.o gsnapl_ssse3-intersect-concordance-uint8.o gsnapl_ssse3-kmer-search.o gsnapl_ssse3-extension-search.o gsnapl_ssse3-repetitive.o gsnapl_ssse3-uint8table.o gsnapl_ssse3-stage1hr.o gsnapl_ssse3-stage1hr-single.o gsnapl_ssse3-stage1hr-paired.o gsnapl_ssse3-uint8tableuint.o gsnapl_ssse3-tableuint.o gsnapl_ssse3-single-cell.o gsnapl_ssse3-request.o gsnapl_ssse3-resulthr.o gsnapl_ssse3-output.o gsnapl_ssse3-inbuffer.o gsnapl_ssse3-samheader.o gsnapl_ssse3-printbuffer.o gsnapl_ssse3-outbuffer.o gsnapl_ssse3-uint8pairtable.o gsnapl_ssse3-splice-count.o gsnapl_ssse3-support.o gsnapl_ssse3-datadir.o gsnapl_ssse3-parserange.o gsnapl_ssse3-getline.o gsnapl_ssse3-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat chmod +x gmap_build chmod +x gmap_process chmod +x gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords chmod +x md_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns chmod +x psl_splicesites chmod +x psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes chmod +x psl_genes chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_splicesites chmod +x gtf_introns chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_introns chmod +x gff3_genes chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' dh_auto_build --builddir build_sse41 cd build_sse41 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'IIT_read': ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c: In function 'read_tree': ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c: In function 'put_compressed_one': In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path.o `test -f 'path.c' || echo '../../src/'`path.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple_large': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse41 gmap_sse41-except.o gmap_sse41-assert.o gmap_sse41-mem.o gmap_sse41-intlist.o gmap_sse41-uintlist.o gmap_sse41-list.o gmap_sse41-littleendian.o gmap_sse41-bigendian.o gmap_sse41-univinterval.o gmap_sse41-interval.o gmap_sse41-stopwatch.o gmap_sse41-semaphore.o gmap_sse41-access.o gmap_sse41-filestring.o gmap_sse41-iit-read-univ.o gmap_sse41-iit-read.o gmap_sse41-md5.o gmap_sse41-bzip2.o gmap_sse41-fopen.o gmap_sse41-sequence.o gmap_sse41-reader.o gmap_sse41-genomicpos.o gmap_sse41-compress.o gmap_sse41-compress-write.o gmap_sse41-gbuffer.o gmap_sse41-genome.o gmap_sse41-popcount.o gmap_sse41-dinucl_bits.o gmap_sse41-genome_canonical.o gmap_sse41-genome-write.o gmap_sse41-bitpack64-read.o gmap_sse41-bitpack64-readtwo.o gmap_sse41-indexdb.o gmap_sse41-oligo.o gmap_sse41-block.o gmap_sse41-chrom.o gmap_sse41-segmentpos.o gmap_sse41-chrnum.o gmap_sse41-uinttable_rh.o gmap_sse41-gregion.o gmap_sse41-match.o gmap_sse41-matchpool.o gmap_sse41-diagnostic.o gmap_sse41-stage1.o gmap_sse41-diag.o gmap_sse41-diagpool.o gmap_sse41-cmet.o gmap_sse41-atoi.o gmap_sse41-orderstat.o gmap_sse41-oligoindex_hr.o gmap_sse41-intron.o gmap_sse41-maxent.o gmap_sse41-maxent_hr.o gmap_sse41-pair.o gmap_sse41-pairpool.o gmap_sse41-cellpool.o gmap_sse41-stage2.o gmap_sse41-doublelist.o gmap_sse41-smooth.o gmap_sse41-splicestringpool.o gmap_sse41-splicetrie_build.o gmap_sse41-splicetrie.o gmap_sse41-boyer-moore.o gmap_sse41-dynprog.o gmap_sse41-dynprog_simd.o gmap_sse41-dynprog_single.o gmap_sse41-dynprog_genome.o gmap_sse41-dynprog_cdna.o gmap_sse41-dynprog_end.o gmap_sse41-translation.o gmap_sse41-pbinom.o gmap_sse41-changepoint.o gmap_sse41-stage3.o gmap_sse41-request.o gmap_sse41-result.o gmap_sse41-output.o gmap_sse41-inbuffer.o gmap_sse41-samheader.o gmap_sse41-printbuffer.o gmap_sse41-outbuffer.o gmap_sse41-chimera.o gmap_sse41-datadir.o gmap_sse41-parserange.o gmap_sse41-getline.o gmap_sse41-gmap.o -lz -lbz2 -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse41 gmapl_sse41-except.o gmapl_sse41-assert.o gmapl_sse41-mem.o gmapl_sse41-intlist.o gmapl_sse41-uintlist.o gmapl_sse41-uint8list.o gmapl_sse41-list.o gmapl_sse41-littleendian.o gmapl_sse41-bigendian.o gmapl_sse41-univinterval.o gmapl_sse41-interval.o gmapl_sse41-stopwatch.o gmapl_sse41-semaphore.o gmapl_sse41-access.o gmapl_sse41-filestring.o gmapl_sse41-iit-read-univ.o gmapl_sse41-iit-read.o gmapl_sse41-md5.o gmapl_sse41-bzip2.o gmapl_sse41-fopen.o gmapl_sse41-sequence.o gmapl_sse41-reader.o gmapl_sse41-genomicpos.o gmapl_sse41-compress.o gmapl_sse41-compress-write.o gmapl_sse41-gbuffer.o gmapl_sse41-genome.o gmapl_sse41-popcount.o gmapl_sse41-dinucl_bits.o gmapl_sse41-genome_canonical.o gmapl_sse41-genome-write.o gmapl_sse41-bitpack64-read.o gmapl_sse41-bitpack64-readtwo.o gmapl_sse41-indexdb.o gmapl_sse41-oligo.o gmapl_sse41-block.o gmapl_sse41-chrom.o gmapl_sse41-segmentpos.o gmapl_sse41-chrnum.o gmapl_sse41-uinttable_rh.o gmapl_sse41-uint8table_rh.o gmapl_sse41-gregion.o gmapl_sse41-match.o gmapl_sse41-matchpool.o gmapl_sse41-diagnostic.o gmapl_sse41-stage1.o gmapl_sse41-diag.o gmapl_sse41-diagpool.o gmapl_sse41-cmet.o gmapl_sse41-atoi.o gmapl_sse41-orderstat.o gmapl_sse41-oligoindex_hr.o gmapl_sse41-intron.o gmapl_sse41-maxent.o gmapl_sse41-maxent_hr.o gmapl_sse41-pair.o gmapl_sse41-pairpool.o gmapl_sse41-cellpool.o gmapl_sse41-stage2.o gmapl_sse41-doublelist.o gmapl_sse41-smooth.o gmapl_sse41-splicestringpool.o gmapl_sse41-splicetrie_build.o gmapl_sse41-splicetrie.o gmapl_sse41-boyer-moore.o gmapl_sse41-dynprog.o gmapl_sse41-dynprog_simd.o gmapl_sse41-dynprog_single.o gmapl_sse41-dynprog_genome.o gmapl_sse41-dynprog_cdna.o gmapl_sse41-dynprog_end.o gmapl_sse41-translation.o gmapl_sse41-pbinom.o gmapl_sse41-changepoint.o gmapl_sse41-stage3.o gmapl_sse41-request.o gmapl_sse41-result.o gmapl_sse41-output.o gmapl_sse41-inbuffer.o gmapl_sse41-samheader.o gmapl_sse41-printbuffer.o gmapl_sse41-outbuffer.o gmapl_sse41-chimera.o gmapl_sse41-datadir.o gmapl_sse41-parserange.o gmapl_sse41-getline.o gmapl_sse41-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse41 gsnap_sse41-except.o gsnap_sse41-assert.o gsnap_sse41-mem.o gsnap_sse41-intlist.o gsnap_sse41-uintlist.o gsnap_sse41-list.o gsnap_sse41-littleendian.o gsnap_sse41-bigendian.o gsnap_sse41-univinterval.o gsnap_sse41-interval.o gsnap_sse41-stopwatch.o gsnap_sse41-semaphore.o gsnap_sse41-access.o gsnap_sse41-filestring.o gsnap_sse41-iit-read-univ.o gsnap_sse41-iit-read.o gsnap_sse41-bzip2.o gsnap_sse41-reader.o gsnap_sse41-genomicpos.o gsnap_sse41-compress.o gsnap_sse41-genome.o gsnap_sse41-transcriptome.o gsnap_sse41-popcount.o gsnap_sse41-genomebits.o gsnap_sse41-genomebits_consec.o gsnap_sse41-genomebits_count.o gsnap_sse41-genomebits_kmer.o gsnap_sse41-genomebits_indel.o gsnap_sse41-genomebits_decode.o gsnap_sse41-genomebits_mismatches.o gsnap_sse41-genomebits_trim.o gsnap_sse41-dinucl_bits.o gsnap_sse41-genome_sites.o gsnap_sse41-bitpack64-read.o gsnap_sse41-bitpack64-readtwo.o gsnap_sse41-mergeinfo.o gsnap_sse41-merge-diagonals-heap-uint4.o gsnap_sse41-merge-uint4.o gsnap_sse41-merge-diagonals-simd-uint4.o gsnap_sse41-indexdb.o gsnap_sse41-localdb-read.o gsnap_sse41-oligo.o gsnap_sse41-chrnum.o gsnap_sse41-maxent_hr.o gsnap_sse41-mapq.o gsnap_sse41-fopen.o gsnap_sse41-shortread.o gsnap_sse41-junction.o gsnap_sse41-concordance.o gsnap_sse41-simplepair.o gsnap_sse41-orderstat.o gsnap_sse41-intlistpool.o gsnap_sse41-uintlistpool.o gsnap_sse41-listpool.o gsnap_sse41-hitlistpool.o gsnap_sse41-pathpool.o gsnap_sse41-auxinfopool.o gsnap_sse41-pathstorepool.o gsnap_sse41-intron.o gsnap_sse41-gbuffer.o gsnap_sse41-select64-common.o gsnap_sse41-select64-ones.o gsnap_sse41-select64-zeroes.o gsnap_sse41-ef64.o gsnap_sse41-nr-x.o gsnap_sse41-knownsplicing.o gsnap_sse41-knownindels.o gsnap_sse41-splice.o gsnap_sse41-indel.o gsnap_sse41-spliceendsgen.o gsnap_sse41-spliceends.o gsnap_sse41-bitpack64-access.o gsnap_sse41-trdiag.o gsnap_sse41-trdiagpool.o gsnap_sse41-tr-extension-search.o gsnap_sse41-univdiag.o gsnap_sse41-univdiagpool.o gsnap_sse41-sedgesort.o gsnap_sse41-auxinfo.o gsnap_sse41-pathstore.o gsnap_sse41-altsplice.o gsnap_sse41-path.o gsnap_sse41-pathpair.o gsnap_sse41-path-solve.o gsnap_sse41-path-fusion.o gsnap_sse41-path-trim.o gsnap_sse41-path-eval.o gsnap_sse41-pathpair-eval.o gsnap_sse41-path-print-alignment.o gsnap_sse41-path-print-m8.o gsnap_sse41-path-print-sam.o gsnap_sse41-path-learn.o gsnap_sse41-method.o gsnap_sse41-doublelist.o gsnap_sse41-bitvector.o gsnap_sse41-transcriptpool.o gsnap_sse41-exon.o gsnap_sse41-transcript.o gsnap_sse41-trpathpool.o gsnap_sse41-trpath.o gsnap_sse41-trpath-solve.o gsnap_sse41-trpath-convert.o gsnap_sse41-trpath-eval.o gsnap_sse41-transcriptome-search.o gsnap_sse41-vectorpool.o gsnap_sse41-repair.o gsnap_sse41-transcript-remap.o gsnap_sse41-transcript-velocity.o gsnap_sse41-intersect-small.o gsnap_sse41-intersect-uint2.o gsnap_sse41-intersect-approx-uint4.o gsnap_sse41-intersect-approx-indices-uint4.o gsnap_sse41-intersect-wdups-indices.o gsnap_sse41-intersect-lower-small.o gsnap_sse41-intersect-higher-small.o gsnap_sse41-intersect-indices-small.o gsnap_sse41-intersect-indices2-small.o gsnap_sse41-intersect-concordance-uint4.o gsnap_sse41-kmer-search.o gsnap_sse41-extension-search.o gsnap_sse41-repetitive.o gsnap_sse41-uint8table.o gsnap_sse41-uinttable.o gsnap_sse41-stage1hr.o gsnap_sse41-stage1hr-single.o gsnap_sse41-stage1hr-paired.o gsnap_sse41-uinttableuint.o gsnap_sse41-tableuint.o gsnap_sse41-single-cell.o gsnap_sse41-request.o gsnap_sse41-resulthr.o gsnap_sse41-output.o gsnap_sse41-inbuffer.o gsnap_sse41-samheader.o gsnap_sse41-printbuffer.o gsnap_sse41-outbuffer.o gsnap_sse41-uintpairtable.o gsnap_sse41-splice-count.o gsnap_sse41-support.o gsnap_sse41-datadir.o gsnap_sse41-parserange.o gsnap_sse41-getline.o gsnap_sse41-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse41 gsnapl_sse41-except.o gsnapl_sse41-assert.o gsnapl_sse41-mem.o gsnapl_sse41-intlist.o gsnapl_sse41-uintlist.o gsnapl_sse41-uint8list.o gsnapl_sse41-list.o gsnapl_sse41-littleendian.o gsnapl_sse41-bigendian.o gsnapl_sse41-univinterval.o gsnapl_sse41-interval.o gsnapl_sse41-stopwatch.o gsnapl_sse41-semaphore.o gsnapl_sse41-access.o gsnapl_sse41-filestring.o gsnapl_sse41-iit-read-univ.o gsnapl_sse41-iit-read.o gsnapl_sse41-bzip2.o gsnapl_sse41-reader.o gsnapl_sse41-genomicpos.o gsnapl_sse41-compress.o gsnapl_sse41-genome.o gsnapl_sse41-transcriptome.o gsnapl_sse41-popcount.o gsnapl_sse41-genomebits.o gsnapl_sse41-genomebits_consec.o gsnapl_sse41-genomebits_count.o gsnapl_sse41-genomebits_kmer.o gsnapl_sse41-genomebits_indel.o gsnapl_sse41-genomebits_decode.o gsnapl_sse41-genomebits_mismatches.o gsnapl_sse41-genomebits_trim.o gsnapl_sse41-dinucl_bits.o gsnapl_sse41-genome_sites.o gsnapl_sse41-bitpack64-read.o gsnapl_sse41-bitpack64-readtwo.o gsnapl_sse41-mergeinfo.o gsnapl_sse41-merge-diagonals-heap-uint8.o gsnapl_sse41-merge-uint8.o gsnapl_sse41-merge-diagonals-simd-uint8.o gsnapl_sse41-merge-diagonals-heap-uint4.o gsnapl_sse41-merge-uint4.o gsnapl_sse41-merge-diagonals-simd-uint4.o gsnapl_sse41-indexdb.o gsnapl_sse41-localdb-read.o gsnapl_sse41-oligo.o gsnapl_sse41-chrnum.o gsnapl_sse41-maxent_hr.o gsnapl_sse41-mapq.o gsnapl_sse41-fopen.o gsnapl_sse41-shortread.o gsnapl_sse41-junction.o gsnapl_sse41-concordance.o gsnapl_sse41-simplepair.o gsnapl_sse41-orderstat.o gsnapl_sse41-intlistpool.o gsnapl_sse41-uintlistpool.o gsnapl_sse41-uint8listpool.o gsnapl_sse41-listpool.o gsnapl_sse41-hitlistpool.o gsnapl_sse41-pathpool.o gsnapl_sse41-auxinfopool.o gsnapl_sse41-pathstorepool.o gsnapl_sse41-intron.o gsnapl_sse41-gbuffer.o gsnapl_sse41-select64-common.o gsnapl_sse41-select64-ones.o gsnapl_sse41-select64-zeroes.o gsnapl_sse41-ef64.o gsnapl_sse41-nr-x.o gsnapl_sse41-knownsplicing.o gsnapl_sse41-knownindels.o gsnapl_sse41-splice.o gsnapl_sse41-indel.o gsnapl_sse41-spliceendsgen.o gsnapl_sse41-spliceends.o gsnapl_sse41-bitpack64-access.o gsnapl_sse41-trdiag.o gsnapl_sse41-trdiagpool.o gsnapl_sse41-tr-extension-search.o gsnapl_sse41-univdiag.o gsnapl_sse41-univdiagpool.o gsnapl_sse41-sedgesort.o gsnapl_sse41-auxinfo.o gsnapl_sse41-pathstore.o gsnapl_sse41-altsplice.o gsnapl_sse41-path.o gsnapl_sse41-pathpair.o gsnapl_sse41-path-solve.o gsnapl_sse41-path-fusion.o gsnapl_sse41-path-trim.o gsnapl_sse41-path-eval.o gsnapl_sse41-pathpair-eval.o gsnapl_sse41-path-print-alignment.o gsnapl_sse41-path-print-m8.o gsnapl_sse41-path-print-sam.o gsnapl_sse41-path-learn.o gsnapl_sse41-method.o gsnapl_sse41-doublelist.o gsnapl_sse41-bitvector.o gsnapl_sse41-transcriptpool.o gsnapl_sse41-exon.o gsnapl_sse41-transcript.o gsnapl_sse41-trpathpool.o gsnapl_sse41-trpath.o gsnapl_sse41-trpath-solve.o gsnapl_sse41-trpath-convert.o gsnapl_sse41-trpath-eval.o gsnapl_sse41-transcriptome-search.o gsnapl_sse41-vectorpool.o gsnapl_sse41-repair.o gsnapl_sse41-transcript-remap.o gsnapl_sse41-transcript-velocity.o gsnapl_sse41-intersect-large.o gsnapl_sse41-intersect-small.o gsnapl_sse41-intersect-uint2.o gsnapl_sse41-intersect-approx-uint4.o gsnapl_sse41-intersect-approx-uint8.o gsnapl_sse41-intersect-approx-indices-uint8.o gsnapl_sse41-intersect-wdups-indices.o gsnapl_sse41-intersect-lower-large.o gsnapl_sse41-intersect-higher-large.o gsnapl_sse41-intersect-indices-small.o gsnapl_sse41-intersect-indices2-large.o gsnapl_sse41-intersect-indices-uint8.o gsnapl_sse41-intersect-concordance-uint8.o gsnapl_sse41-kmer-search.o gsnapl_sse41-extension-search.o gsnapl_sse41-repetitive.o gsnapl_sse41-uint8table.o gsnapl_sse41-stage1hr.o gsnapl_sse41-stage1hr-single.o gsnapl_sse41-stage1hr-paired.o gsnapl_sse41-uint8tableuint.o gsnapl_sse41-tableuint.o gsnapl_sse41-single-cell.o gsnapl_sse41-request.o gsnapl_sse41-resulthr.o gsnapl_sse41-output.o gsnapl_sse41-inbuffer.o gsnapl_sse41-samheader.o gsnapl_sse41-printbuffer.o gsnapl_sse41-outbuffer.o gsnapl_sse41-uint8pairtable.o gsnapl_sse41-splice-count.o gsnapl_sse41-support.o gsnapl_sse41-datadir.o gsnapl_sse41-parserange.o gsnapl_sse41-getline.o gsnapl_sse41-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords chmod +x md_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x psl_splicesites chmod +x psl_introns chmod +x psl_genes chmod +x ensembl_genes chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_introns cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes chmod +x gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_introns cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x gff3_genes chmod +x dbsnp_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' dh_auto_build --builddir build_sse42 cd build_sse42 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/iit-read.c: In function 'read_tree': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/compress-write.c: In function 'put_compressed_one': ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c ../../src/indexdb.c: In function 'positions_read_multiple': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse42 gmap_sse42-except.o gmap_sse42-assert.o gmap_sse42-mem.o gmap_sse42-intlist.o gmap_sse42-uintlist.o gmap_sse42-list.o gmap_sse42-littleendian.o gmap_sse42-bigendian.o gmap_sse42-univinterval.o gmap_sse42-interval.o gmap_sse42-stopwatch.o gmap_sse42-semaphore.o gmap_sse42-access.o gmap_sse42-filestring.o gmap_sse42-iit-read-univ.o gmap_sse42-iit-read.o gmap_sse42-md5.o gmap_sse42-bzip2.o gmap_sse42-fopen.o gmap_sse42-sequence.o gmap_sse42-reader.o gmap_sse42-genomicpos.o gmap_sse42-compress.o gmap_sse42-compress-write.o gmap_sse42-gbuffer.o gmap_sse42-genome.o gmap_sse42-popcount.o gmap_sse42-dinucl_bits.o gmap_sse42-genome_canonical.o gmap_sse42-genome-write.o gmap_sse42-bitpack64-read.o gmap_sse42-bitpack64-readtwo.o gmap_sse42-indexdb.o gmap_sse42-oligo.o gmap_sse42-block.o gmap_sse42-chrom.o gmap_sse42-segmentpos.o gmap_sse42-chrnum.o gmap_sse42-uinttable_rh.o gmap_sse42-gregion.o gmap_sse42-match.o gmap_sse42-matchpool.o gmap_sse42-diagnostic.o gmap_sse42-stage1.o gmap_sse42-diag.o gmap_sse42-diagpool.o gmap_sse42-cmet.o gmap_sse42-atoi.o gmap_sse42-orderstat.o gmap_sse42-oligoindex_hr.o gmap_sse42-intron.o gmap_sse42-maxent.o gmap_sse42-maxent_hr.o gmap_sse42-pair.o gmap_sse42-pairpool.o gmap_sse42-cellpool.o gmap_sse42-stage2.o gmap_sse42-doublelist.o gmap_sse42-smooth.o gmap_sse42-splicestringpool.o gmap_sse42-splicetrie_build.o gmap_sse42-splicetrie.o gmap_sse42-boyer-moore.o gmap_sse42-dynprog.o gmap_sse42-dynprog_simd.o gmap_sse42-dynprog_single.o gmap_sse42-dynprog_genome.o gmap_sse42-dynprog_cdna.o gmap_sse42-dynprog_end.o gmap_sse42-translation.o gmap_sse42-pbinom.o gmap_sse42-changepoint.o gmap_sse42-stage3.o gmap_sse42-request.o gmap_sse42-result.o gmap_sse42-output.o gmap_sse42-inbuffer.o gmap_sse42-samheader.o gmap_sse42-printbuffer.o gmap_sse42-outbuffer.o gmap_sse42-chimera.o gmap_sse42-datadir.o gmap_sse42-parserange.o gmap_sse42-getline.o gmap_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse42 gmapl_sse42-except.o gmapl_sse42-assert.o gmapl_sse42-mem.o gmapl_sse42-intlist.o gmapl_sse42-uintlist.o gmapl_sse42-uint8list.o gmapl_sse42-list.o gmapl_sse42-littleendian.o gmapl_sse42-bigendian.o gmapl_sse42-univinterval.o gmapl_sse42-interval.o gmapl_sse42-stopwatch.o gmapl_sse42-semaphore.o gmapl_sse42-access.o gmapl_sse42-filestring.o gmapl_sse42-iit-read-univ.o gmapl_sse42-iit-read.o gmapl_sse42-md5.o gmapl_sse42-bzip2.o gmapl_sse42-fopen.o gmapl_sse42-sequence.o gmapl_sse42-reader.o gmapl_sse42-genomicpos.o gmapl_sse42-compress.o gmapl_sse42-compress-write.o gmapl_sse42-gbuffer.o gmapl_sse42-genome.o gmapl_sse42-popcount.o gmapl_sse42-dinucl_bits.o gmapl_sse42-genome_canonical.o gmapl_sse42-genome-write.o gmapl_sse42-bitpack64-read.o gmapl_sse42-bitpack64-readtwo.o gmapl_sse42-indexdb.o gmapl_sse42-oligo.o gmapl_sse42-block.o gmapl_sse42-chrom.o gmapl_sse42-segmentpos.o gmapl_sse42-chrnum.o gmapl_sse42-uinttable_rh.o gmapl_sse42-uint8table_rh.o gmapl_sse42-gregion.o gmapl_sse42-match.o gmapl_sse42-matchpool.o gmapl_sse42-diagnostic.o gmapl_sse42-stage1.o gmapl_sse42-diag.o gmapl_sse42-diagpool.o gmapl_sse42-cmet.o gmapl_sse42-atoi.o gmapl_sse42-orderstat.o gmapl_sse42-oligoindex_hr.o gmapl_sse42-intron.o gmapl_sse42-maxent.o gmapl_sse42-maxent_hr.o gmapl_sse42-pair.o gmapl_sse42-pairpool.o gmapl_sse42-cellpool.o gmapl_sse42-stage2.o gmapl_sse42-doublelist.o gmapl_sse42-smooth.o gmapl_sse42-splicestringpool.o gmapl_sse42-splicetrie_build.o gmapl_sse42-splicetrie.o gmapl_sse42-boyer-moore.o gmapl_sse42-dynprog.o gmapl_sse42-dynprog_simd.o gmapl_sse42-dynprog_single.o gmapl_sse42-dynprog_genome.o gmapl_sse42-dynprog_cdna.o gmapl_sse42-dynprog_end.o gmapl_sse42-translation.o gmapl_sse42-pbinom.o gmapl_sse42-changepoint.o gmapl_sse42-stage3.o gmapl_sse42-request.o gmapl_sse42-result.o gmapl_sse42-output.o gmapl_sse42-inbuffer.o gmapl_sse42-samheader.o gmapl_sse42-printbuffer.o gmapl_sse42-outbuffer.o gmapl_sse42-chimera.o gmapl_sse42-datadir.o gmapl_sse42-parserange.o gmapl_sse42-getline.o gmapl_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse42 gsnap_sse42-except.o gsnap_sse42-assert.o gsnap_sse42-mem.o gsnap_sse42-intlist.o gsnap_sse42-uintlist.o gsnap_sse42-list.o gsnap_sse42-littleendian.o gsnap_sse42-bigendian.o gsnap_sse42-univinterval.o gsnap_sse42-interval.o gsnap_sse42-stopwatch.o gsnap_sse42-semaphore.o gsnap_sse42-access.o gsnap_sse42-filestring.o gsnap_sse42-iit-read-univ.o gsnap_sse42-iit-read.o gsnap_sse42-bzip2.o gsnap_sse42-reader.o gsnap_sse42-genomicpos.o gsnap_sse42-compress.o gsnap_sse42-genome.o gsnap_sse42-transcriptome.o gsnap_sse42-popcount.o gsnap_sse42-genomebits.o gsnap_sse42-genomebits_consec.o gsnap_sse42-genomebits_count.o gsnap_sse42-genomebits_kmer.o gsnap_sse42-genomebits_indel.o gsnap_sse42-genomebits_decode.o gsnap_sse42-genomebits_mismatches.o gsnap_sse42-genomebits_trim.o gsnap_sse42-dinucl_bits.o gsnap_sse42-genome_sites.o gsnap_sse42-bitpack64-read.o gsnap_sse42-bitpack64-readtwo.o gsnap_sse42-mergeinfo.o gsnap_sse42-merge-diagonals-heap-uint4.o gsnap_sse42-merge-uint4.o gsnap_sse42-merge-diagonals-simd-uint4.o gsnap_sse42-indexdb.o gsnap_sse42-localdb-read.o gsnap_sse42-oligo.o gsnap_sse42-chrnum.o gsnap_sse42-maxent_hr.o gsnap_sse42-mapq.o gsnap_sse42-fopen.o gsnap_sse42-shortread.o gsnap_sse42-junction.o gsnap_sse42-concordance.o gsnap_sse42-simplepair.o gsnap_sse42-orderstat.o gsnap_sse42-intlistpool.o gsnap_sse42-uintlistpool.o gsnap_sse42-listpool.o gsnap_sse42-hitlistpool.o gsnap_sse42-pathpool.o gsnap_sse42-auxinfopool.o gsnap_sse42-pathstorepool.o gsnap_sse42-intron.o gsnap_sse42-gbuffer.o gsnap_sse42-select64-common.o gsnap_sse42-select64-ones.o gsnap_sse42-select64-zeroes.o gsnap_sse42-ef64.o gsnap_sse42-nr-x.o gsnap_sse42-knownsplicing.o gsnap_sse42-knownindels.o gsnap_sse42-splice.o gsnap_sse42-indel.o gsnap_sse42-spliceendsgen.o gsnap_sse42-spliceends.o gsnap_sse42-bitpack64-access.o gsnap_sse42-trdiag.o gsnap_sse42-trdiagpool.o gsnap_sse42-tr-extension-search.o gsnap_sse42-univdiag.o gsnap_sse42-univdiagpool.o gsnap_sse42-sedgesort.o gsnap_sse42-auxinfo.o gsnap_sse42-pathstore.o gsnap_sse42-altsplice.o gsnap_sse42-path.o gsnap_sse42-pathpair.o gsnap_sse42-path-solve.o gsnap_sse42-path-fusion.o gsnap_sse42-path-trim.o gsnap_sse42-path-eval.o gsnap_sse42-pathpair-eval.o gsnap_sse42-path-print-alignment.o gsnap_sse42-path-print-m8.o gsnap_sse42-path-print-sam.o gsnap_sse42-path-learn.o gsnap_sse42-method.o gsnap_sse42-doublelist.o gsnap_sse42-bitvector.o gsnap_sse42-transcriptpool.o gsnap_sse42-exon.o gsnap_sse42-transcript.o gsnap_sse42-trpathpool.o gsnap_sse42-trpath.o gsnap_sse42-trpath-solve.o gsnap_sse42-trpath-convert.o gsnap_sse42-trpath-eval.o gsnap_sse42-transcriptome-search.o gsnap_sse42-vectorpool.o gsnap_sse42-repair.o gsnap_sse42-transcript-remap.o gsnap_sse42-transcript-velocity.o gsnap_sse42-intersect-small.o gsnap_sse42-intersect-uint2.o gsnap_sse42-intersect-approx-uint4.o gsnap_sse42-intersect-approx-indices-uint4.o gsnap_sse42-intersect-wdups-indices.o gsnap_sse42-intersect-lower-small.o gsnap_sse42-intersect-higher-small.o gsnap_sse42-intersect-indices-small.o gsnap_sse42-intersect-indices2-small.o gsnap_sse42-intersect-concordance-uint4.o gsnap_sse42-kmer-search.o gsnap_sse42-extension-search.o gsnap_sse42-repetitive.o gsnap_sse42-uint8table.o gsnap_sse42-uinttable.o gsnap_sse42-stage1hr.o gsnap_sse42-stage1hr-single.o gsnap_sse42-stage1hr-paired.o gsnap_sse42-uinttableuint.o gsnap_sse42-tableuint.o gsnap_sse42-single-cell.o gsnap_sse42-request.o gsnap_sse42-resulthr.o gsnap_sse42-output.o gsnap_sse42-inbuffer.o gsnap_sse42-samheader.o gsnap_sse42-printbuffer.o gsnap_sse42-outbuffer.o gsnap_sse42-uintpairtable.o gsnap_sse42-splice-count.o gsnap_sse42-support.o gsnap_sse42-datadir.o gsnap_sse42-parserange.o gsnap_sse42-getline.o gsnap_sse42-gsnap.o -lz -lbz2 -lm ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse42 gsnapl_sse42-except.o gsnapl_sse42-assert.o gsnapl_sse42-mem.o gsnapl_sse42-intlist.o gsnapl_sse42-uintlist.o gsnapl_sse42-uint8list.o gsnapl_sse42-list.o gsnapl_sse42-littleendian.o gsnapl_sse42-bigendian.o gsnapl_sse42-univinterval.o gsnapl_sse42-interval.o gsnapl_sse42-stopwatch.o gsnapl_sse42-semaphore.o gsnapl_sse42-access.o gsnapl_sse42-filestring.o gsnapl_sse42-iit-read-univ.o gsnapl_sse42-iit-read.o gsnapl_sse42-bzip2.o gsnapl_sse42-reader.o gsnapl_sse42-genomicpos.o gsnapl_sse42-compress.o gsnapl_sse42-genome.o gsnapl_sse42-transcriptome.o gsnapl_sse42-popcount.o gsnapl_sse42-genomebits.o gsnapl_sse42-genomebits_consec.o gsnapl_sse42-genomebits_count.o gsnapl_sse42-genomebits_kmer.o gsnapl_sse42-genomebits_indel.o gsnapl_sse42-genomebits_decode.o gsnapl_sse42-genomebits_mismatches.o gsnapl_sse42-genomebits_trim.o gsnapl_sse42-dinucl_bits.o gsnapl_sse42-genome_sites.o gsnapl_sse42-bitpack64-read.o gsnapl_sse42-bitpack64-readtwo.o gsnapl_sse42-mergeinfo.o gsnapl_sse42-merge-diagonals-heap-uint8.o gsnapl_sse42-merge-uint8.o gsnapl_sse42-merge-diagonals-simd-uint8.o gsnapl_sse42-merge-diagonals-heap-uint4.o gsnapl_sse42-merge-uint4.o gsnapl_sse42-merge-diagonals-simd-uint4.o gsnapl_sse42-indexdb.o gsnapl_sse42-localdb-read.o gsnapl_sse42-oligo.o gsnapl_sse42-chrnum.o gsnapl_sse42-maxent_hr.o gsnapl_sse42-mapq.o gsnapl_sse42-fopen.o gsnapl_sse42-shortread.o gsnapl_sse42-junction.o gsnapl_sse42-concordance.o gsnapl_sse42-simplepair.o gsnapl_sse42-orderstat.o gsnapl_sse42-intlistpool.o gsnapl_sse42-uintlistpool.o gsnapl_sse42-uint8listpool.o gsnapl_sse42-listpool.o gsnapl_sse42-hitlistpool.o gsnapl_sse42-pathpool.o gsnapl_sse42-auxinfopool.o gsnapl_sse42-pathstorepool.o gsnapl_sse42-intron.o gsnapl_sse42-gbuffer.o gsnapl_sse42-select64-common.o gsnapl_sse42-select64-ones.o gsnapl_sse42-select64-zeroes.o gsnapl_sse42-ef64.o gsnapl_sse42-nr-x.o gsnapl_sse42-knownsplicing.o gsnapl_sse42-knownindels.o gsnapl_sse42-splice.o gsnapl_sse42-indel.o gsnapl_sse42-spliceendsgen.o gsnapl_sse42-spliceends.o gsnapl_sse42-bitpack64-access.o gsnapl_sse42-trdiag.o gsnapl_sse42-trdiagpool.o gsnapl_sse42-tr-extension-search.o gsnapl_sse42-univdiag.o gsnapl_sse42-univdiagpool.o gsnapl_sse42-sedgesort.o gsnapl_sse42-auxinfo.o gsnapl_sse42-pathstore.o gsnapl_sse42-altsplice.o gsnapl_sse42-path.o gsnapl_sse42-pathpair.o gsnapl_sse42-path-solve.o gsnapl_sse42-path-fusion.o gsnapl_sse42-path-trim.o gsnapl_sse42-path-eval.o gsnapl_sse42-pathpair-eval.o gsnapl_sse42-path-print-alignment.o gsnapl_sse42-path-print-m8.o gsnapl_sse42-path-print-sam.o gsnapl_sse42-path-learn.o gsnapl_sse42-method.o gsnapl_sse42-doublelist.o gsnapl_sse42-bitvector.o gsnapl_sse42-transcriptpool.o gsnapl_sse42-exon.o gsnapl_sse42-transcript.o gsnapl_sse42-trpathpool.o gsnapl_sse42-trpath.o gsnapl_sse42-trpath-solve.o gsnapl_sse42-trpath-convert.o gsnapl_sse42-trpath-eval.o gsnapl_sse42-transcriptome-search.o gsnapl_sse42-vectorpool.o gsnapl_sse42-repair.o gsnapl_sse42-transcript-remap.o gsnapl_sse42-transcript-velocity.o gsnapl_sse42-intersect-large.o gsnapl_sse42-intersect-small.o gsnapl_sse42-intersect-uint2.o gsnapl_sse42-intersect-approx-uint4.o gsnapl_sse42-intersect-approx-uint8.o gsnapl_sse42-intersect-approx-indices-uint8.o gsnapl_sse42-intersect-wdups-indices.o gsnapl_sse42-intersect-lower-large.o gsnapl_sse42-intersect-higher-large.o gsnapl_sse42-intersect-indices-small.o gsnapl_sse42-intersect-indices2-large.o gsnapl_sse42-intersect-indices-uint8.o gsnapl_sse42-intersect-concordance-uint8.o gsnapl_sse42-kmer-search.o gsnapl_sse42-extension-search.o gsnapl_sse42-repetitive.o gsnapl_sse42-uint8table.o gsnapl_sse42-stage1hr.o gsnapl_sse42-stage1hr-single.o gsnapl_sse42-stage1hr-paired.o gsnapl_sse42-uint8tableuint.o gsnapl_sse42-tableuint.o gsnapl_sse42-single-cell.o gsnapl_sse42-request.o gsnapl_sse42-resulthr.o gsnapl_sse42-output.o gsnapl_sse42-inbuffer.o gsnapl_sse42-samheader.o gsnapl_sse42-printbuffer.o gsnapl_sse42-outbuffer.o gsnapl_sse42-uint8pairtable.o gsnapl_sse42-splice-count.o gsnapl_sse42-support.o gsnapl_sse42-datadir.o gsnapl_sse42-parserange.o gsnapl_sse42-getline.o gsnapl_sse42-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build chmod +x gmap_process chmod +x gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords chmod +x gmap_cat chmod +x md_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes chmod +x psl_splicesites chmod +x psl_introns chmod +x psl_genes chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites chmod +x gtf_introns cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_introns chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' dh_auto_build --builddir build_avx2 cd build_avx2 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/compress-write.c: In function 'put_compressed_one': In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read.c: In function 'read_tree': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-dinucl_bits.o gmap_avx2-genome_canonical.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-printbuffer.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-dinucl_bits.o gmapl_avx2-genome_canonical.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-uint8table_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-printbuffer.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genomebits.o gsnap_avx2-genomebits_consec.o gsnap_avx2-genomebits_count.o gsnap_avx2-genomebits_kmer.o gsnap_avx2-genomebits_indel.o gsnap_avx2-genomebits_decode.o gsnap_avx2-genomebits_mismatches.o gsnap_avx2-genomebits_trim.o gsnap_avx2-dinucl_bits.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-mergeinfo.o gsnap_avx2-merge-diagonals-heap-uint4.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-localdb-read.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-junction.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-pathpool.o gsnap_avx2-auxinfopool.o gsnap_avx2-pathstorepool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-select64-common.o gsnap_avx2-select64-ones.o gsnap_avx2-select64-zeroes.o gsnap_avx2-ef64.o gsnap_avx2-nr-x.o gsnap_avx2-knownsplicing.o gsnap_avx2-knownindels.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-spliceendsgen.o gsnap_avx2-spliceends.o gsnap_avx2-bitpack64-access.o gsnap_avx2-trdiag.o gsnap_avx2-trdiagpool.o gsnap_avx2-tr-extension-search.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-auxinfo.o gsnap_avx2-pathstore.o gsnap_avx2-altsplice.o gsnap_avx2-path.o gsnap_avx2-pathpair.o gsnap_avx2-path-solve.o gsnap_avx2-path-fusion.o gsnap_avx2-path-trim.o gsnap_avx2-path-eval.o gsnap_avx2-pathpair-eval.o gsnap_avx2-path-print-alignment.o gsnap_avx2-path-print-m8.o gsnap_avx2-path-print-sam.o gsnap_avx2-path-learn.o gsnap_avx2-method.o gsnap_avx2-doublelist.o gsnap_avx2-bitvector.o gsnap_avx2-transcriptpool.o gsnap_avx2-exon.o gsnap_avx2-transcript.o gsnap_avx2-trpathpool.o gsnap_avx2-trpath.o gsnap_avx2-trpath-solve.o gsnap_avx2-trpath-convert.o gsnap_avx2-trpath-eval.o gsnap_avx2-transcriptome-search.o gsnap_avx2-vectorpool.o gsnap_avx2-repair.o gsnap_avx2-transcript-remap.o gsnap_avx2-transcript-velocity.o gsnap_avx2-intersect-small.o gsnap_avx2-intersect-uint2.o gsnap_avx2-intersect-approx-uint4.o gsnap_avx2-intersect-approx-indices-uint4.o gsnap_avx2-intersect-wdups-indices.o gsnap_avx2-intersect-lower-small.o gsnap_avx2-intersect-higher-small.o gsnap_avx2-intersect-indices-small.o gsnap_avx2-intersect-indices2-small.o gsnap_avx2-intersect-concordance-uint4.o gsnap_avx2-kmer-search.o gsnap_avx2-extension-search.o gsnap_avx2-repetitive.o gsnap_avx2-uint8table.o gsnap_avx2-uinttable.o gsnap_avx2-stage1hr.o gsnap_avx2-stage1hr-single.o gsnap_avx2-stage1hr-paired.o gsnap_avx2-uinttableuint.o gsnap_avx2-tableuint.o gsnap_avx2-single-cell.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-printbuffer.o gsnap_avx2-outbuffer.o gsnap_avx2-uintpairtable.o gsnap_avx2-splice-count.o gsnap_avx2-support.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-gsnap.o -lz -lbz2 -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx2 gsnapl_avx2-except.o gsnapl_avx2-assert.o gsnapl_avx2-mem.o gsnapl_avx2-intlist.o gsnapl_avx2-uintlist.o gsnapl_avx2-uint8list.o gsnapl_avx2-list.o gsnapl_avx2-littleendian.o gsnapl_avx2-bigendian.o gsnapl_avx2-univinterval.o gsnapl_avx2-interval.o gsnapl_avx2-stopwatch.o gsnapl_avx2-semaphore.o gsnapl_avx2-access.o gsnapl_avx2-filestring.o gsnapl_avx2-iit-read-univ.o gsnapl_avx2-iit-read.o gsnapl_avx2-bzip2.o gsnapl_avx2-reader.o gsnapl_avx2-genomicpos.o gsnapl_avx2-compress.o gsnapl_avx2-genome.o gsnapl_avx2-transcriptome.o gsnapl_avx2-popcount.o gsnapl_avx2-genomebits.o gsnapl_avx2-genomebits_consec.o gsnapl_avx2-genomebits_count.o gsnapl_avx2-genomebits_kmer.o gsnapl_avx2-genomebits_indel.o gsnapl_avx2-genomebits_decode.o gsnapl_avx2-genomebits_mismatches.o gsnapl_avx2-genomebits_trim.o gsnapl_avx2-dinucl_bits.o gsnapl_avx2-genome_sites.o gsnapl_avx2-bitpack64-read.o gsnapl_avx2-bitpack64-readtwo.o gsnapl_avx2-mergeinfo.o gsnapl_avx2-merge-diagonals-heap-uint8.o gsnapl_avx2-merge-uint8.o gsnapl_avx2-merge-diagonals-simd-uint8.o gsnapl_avx2-merge-diagonals-heap-uint4.o gsnapl_avx2-merge-uint4.o gsnapl_avx2-merge-diagonals-simd-uint4.o gsnapl_avx2-indexdb.o gsnapl_avx2-localdb-read.o gsnapl_avx2-oligo.o gsnapl_avx2-chrnum.o gsnapl_avx2-maxent_hr.o gsnapl_avx2-mapq.o gsnapl_avx2-fopen.o gsnapl_avx2-shortread.o gsnapl_avx2-junction.o gsnapl_avx2-concordance.o gsnapl_avx2-simplepair.o gsnapl_avx2-orderstat.o gsnapl_avx2-intlistpool.o gsnapl_avx2-uintlistpool.o gsnapl_avx2-uint8listpool.o gsnapl_avx2-listpool.o gsnapl_avx2-hitlistpool.o gsnapl_avx2-pathpool.o gsnapl_avx2-auxinfopool.o gsnapl_avx2-pathstorepool.o gsnapl_avx2-intron.o gsnapl_avx2-gbuffer.o gsnapl_avx2-select64-common.o gsnapl_avx2-select64-ones.o gsnapl_avx2-select64-zeroes.o gsnapl_avx2-ef64.o gsnapl_avx2-nr-x.o gsnapl_avx2-knownsplicing.o gsnapl_avx2-knownindels.o gsnapl_avx2-splice.o gsnapl_avx2-indel.o gsnapl_avx2-spliceendsgen.o gsnapl_avx2-spliceends.o gsnapl_avx2-bitpack64-access.o gsnapl_avx2-trdiag.o gsnapl_avx2-trdiagpool.o gsnapl_avx2-tr-extension-search.o gsnapl_avx2-univdiag.o gsnapl_avx2-univdiagpool.o gsnapl_avx2-sedgesort.o gsnapl_avx2-auxinfo.o gsnapl_avx2-pathstore.o gsnapl_avx2-altsplice.o gsnapl_avx2-path.o gsnapl_avx2-pathpair.o gsnapl_avx2-path-solve.o gsnapl_avx2-path-fusion.o gsnapl_avx2-path-trim.o gsnapl_avx2-path-eval.o gsnapl_avx2-pathpair-eval.o gsnapl_avx2-path-print-alignment.o gsnapl_avx2-path-print-m8.o gsnapl_avx2-path-print-sam.o gsnapl_avx2-path-learn.o gsnapl_avx2-method.o gsnapl_avx2-doublelist.o gsnapl_avx2-bitvector.o gsnapl_avx2-transcriptpool.o gsnapl_avx2-exon.o gsnapl_avx2-transcript.o gsnapl_avx2-trpathpool.o gsnapl_avx2-trpath.o gsnapl_avx2-trpath-solve.o gsnapl_avx2-trpath-convert.o gsnapl_avx2-trpath-eval.o gsnapl_avx2-transcriptome-search.o gsnapl_avx2-vectorpool.o gsnapl_avx2-repair.o gsnapl_avx2-transcript-remap.o gsnapl_avx2-transcript-velocity.o gsnapl_avx2-intersect-large.o gsnapl_avx2-intersect-small.o gsnapl_avx2-intersect-uint2.o gsnapl_avx2-intersect-approx-uint4.o gsnapl_avx2-intersect-approx-uint8.o gsnapl_avx2-intersect-approx-indices-uint8.o gsnapl_avx2-intersect-wdups-indices.o gsnapl_avx2-intersect-lower-large.o gsnapl_avx2-intersect-higher-large.o gsnapl_avx2-intersect-indices-small.o gsnapl_avx2-intersect-indices2-large.o gsnapl_avx2-intersect-indices-uint8.o gsnapl_avx2-intersect-concordance-uint8.o gsnapl_avx2-kmer-search.o gsnapl_avx2-extension-search.o gsnapl_avx2-repetitive.o gsnapl_avx2-uint8table.o gsnapl_avx2-stage1hr.o gsnapl_avx2-stage1hr-single.o gsnapl_avx2-stage1hr-paired.o gsnapl_avx2-uint8tableuint.o gsnapl_avx2-tableuint.o gsnapl_avx2-single-cell.o gsnapl_avx2-request.o gsnapl_avx2-resulthr.o gsnapl_avx2-output.o gsnapl_avx2-inbuffer.o gsnapl_avx2-samheader.o gsnapl_avx2-printbuffer.o gsnapl_avx2-outbuffer.o gsnapl_avx2-uint8pairtable.o gsnapl_avx2-splice-count.o gsnapl_avx2-support.o gsnapl_avx2-datadir.o gsnapl_avx2-parserange.o gsnapl_avx2-getline.o gsnapl_avx2-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat chmod +x gmap_build chmod +x gmap_process chmod +x gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords chmod +x md_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x psl_introns chmod +x psl_splicesites chmod +x psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x ensembl_genes cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites cp gtf_genes.pl gtf_genes chmod +x gtf_introns chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites chmod +x gff3_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_genes chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' dh_auto_build --builddir build_avx512 cd build_avx512 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make all-am make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c ../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro 'FREAD_UINT' 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro 'FREAD_UINTS' 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro 'FREAD_UINT' 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro 'FREAD_UINT' 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro 'FREAD_UINTS' 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro 'FREAD_UINTS' 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro 'FREAD_UINT' 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro 'FREAD_UINTS' 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro 'FREAD_UINT' 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro 'FREAD_UINT' 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro 'FREAD_UINTS' 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro 'FREAD_UINT' 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro 'FREAD_UINT' 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro 'FREAD_UINTS' 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/iit_store.c: In function 'parse_fasta': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/md5.c: In function 'MD5_compute': ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function 'fgets', inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function 'Stage1_list_all_univdiagonals': ../../src/stage1hr.c:1359:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx512 gmap_avx512-except.o gmap_avx512-assert.o gmap_avx512-mem.o gmap_avx512-intlist.o gmap_avx512-uintlist.o gmap_avx512-list.o gmap_avx512-littleendian.o gmap_avx512-bigendian.o gmap_avx512-univinterval.o gmap_avx512-interval.o gmap_avx512-stopwatch.o gmap_avx512-semaphore.o gmap_avx512-access.o gmap_avx512-filestring.o gmap_avx512-iit-read-univ.o gmap_avx512-iit-read.o gmap_avx512-md5.o gmap_avx512-bzip2.o gmap_avx512-fopen.o gmap_avx512-sequence.o gmap_avx512-reader.o gmap_avx512-genomicpos.o gmap_avx512-compress.o gmap_avx512-compress-write.o gmap_avx512-gbuffer.o gmap_avx512-genome.o gmap_avx512-popcount.o gmap_avx512-dinucl_bits.o gmap_avx512-genome_canonical.o gmap_avx512-genome-write.o gmap_avx512-bitpack64-read.o gmap_avx512-bitpack64-readtwo.o gmap_avx512-indexdb.o gmap_avx512-oligo.o gmap_avx512-block.o gmap_avx512-chrom.o gmap_avx512-segmentpos.o gmap_avx512-chrnum.o gmap_avx512-uinttable_rh.o gmap_avx512-gregion.o gmap_avx512-match.o gmap_avx512-matchpool.o gmap_avx512-diagnostic.o gmap_avx512-stage1.o gmap_avx512-diag.o gmap_avx512-diagpool.o gmap_avx512-cmet.o gmap_avx512-atoi.o gmap_avx512-orderstat.o gmap_avx512-oligoindex_hr.o gmap_avx512-intron.o gmap_avx512-maxent.o gmap_avx512-maxent_hr.o gmap_avx512-pair.o gmap_avx512-pairpool.o gmap_avx512-cellpool.o gmap_avx512-stage2.o gmap_avx512-doublelist.o gmap_avx512-smooth.o gmap_avx512-splicestringpool.o gmap_avx512-splicetrie_build.o gmap_avx512-splicetrie.o gmap_avx512-boyer-moore.o gmap_avx512-dynprog.o gmap_avx512-dynprog_simd.o gmap_avx512-dynprog_single.o gmap_avx512-dynprog_genome.o gmap_avx512-dynprog_cdna.o gmap_avx512-dynprog_end.o gmap_avx512-translation.o gmap_avx512-pbinom.o gmap_avx512-changepoint.o gmap_avx512-stage3.o gmap_avx512-request.o gmap_avx512-result.o gmap_avx512-output.o gmap_avx512-inbuffer.o gmap_avx512-samheader.o gmap_avx512-printbuffer.o gmap_avx512-outbuffer.o gmap_avx512-chimera.o gmap_avx512-datadir.o gmap_avx512-parserange.o gmap_avx512-getline.o gmap_avx512-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx512 gsnap_avx512-except.o gsnap_avx512-assert.o gsnap_avx512-mem.o gsnap_avx512-intlist.o gsnap_avx512-uintlist.o gsnap_avx512-list.o gsnap_avx512-littleendian.o gsnap_avx512-bigendian.o gsnap_avx512-univinterval.o gsnap_avx512-interval.o gsnap_avx512-stopwatch.o gsnap_avx512-semaphore.o gsnap_avx512-access.o gsnap_avx512-filestring.o gsnap_avx512-iit-read-univ.o gsnap_avx512-iit-read.o gsnap_avx512-bzip2.o gsnap_avx512-reader.o gsnap_avx512-genomicpos.o gsnap_avx512-compress.o gsnap_avx512-genome.o gsnap_avx512-transcriptome.o gsnap_avx512-popcount.o gsnap_avx512-genomebits.o gsnap_avx512-genomebits_consec.o gsnap_avx512-genomebits_count.o gsnap_avx512-genomebits_kmer.o gsnap_avx512-genomebits_indel.o gsnap_avx512-genomebits_decode.o gsnap_avx512-genomebits_mismatches.o gsnap_avx512-genomebits_trim.o gsnap_avx512-dinucl_bits.o gsnap_avx512-genome_sites.o gsnap_avx512-bitpack64-read.o gsnap_avx512-bitpack64-readtwo.o gsnap_avx512-mergeinfo.o gsnap_avx512-merge-diagonals-heap-uint4.o gsnap_avx512-merge-uint4.o gsnap_avx512-merge-diagonals-simd-uint4.o gsnap_avx512-indexdb.o gsnap_avx512-localdb-read.o gsnap_avx512-oligo.o gsnap_avx512-chrnum.o gsnap_avx512-maxent_hr.o gsnap_avx512-mapq.o gsnap_avx512-fopen.o gsnap_avx512-shortread.o gsnap_avx512-junction.o gsnap_avx512-concordance.o gsnap_avx512-simplepair.o gsnap_avx512-orderstat.o gsnap_avx512-intlistpool.o gsnap_avx512-uintlistpool.o gsnap_avx512-listpool.o gsnap_avx512-hitlistpool.o gsnap_avx512-pathpool.o gsnap_avx512-auxinfopool.o gsnap_avx512-pathstorepool.o gsnap_avx512-intron.o gsnap_avx512-gbuffer.o gsnap_avx512-select64-common.o gsnap_avx512-select64-ones.o gsnap_avx512-select64-zeroes.o gsnap_avx512-ef64.o gsnap_avx512-nr-x.o gsnap_avx512-knownsplicing.o gsnap_avx512-knownindels.o gsnap_avx512-splice.o gsnap_avx512-indel.o gsnap_avx512-spliceendsgen.o gsnap_avx512-spliceends.o gsnap_avx512-bitpack64-access.o gsnap_avx512-trdiag.o gsnap_avx512-trdiagpool.o gsnap_avx512-tr-extension-search.o gsnap_avx512-univdiag.o gsnap_avx512-univdiagpool.o gsnap_avx512-sedgesort.o gsnap_avx512-auxinfo.o gsnap_avx512-pathstore.o gsnap_avx512-altsplice.o gsnap_avx512-path.o gsnap_avx512-pathpair.o gsnap_avx512-path-solve.o gsnap_avx512-path-fusion.o gsnap_avx512-path-trim.o gsnap_avx512-path-eval.o gsnap_avx512-pathpair-eval.o gsnap_avx512-path-print-alignment.o gsnap_avx512-path-print-m8.o gsnap_avx512-path-print-sam.o gsnap_avx512-path-learn.o gsnap_avx512-method.o gsnap_avx512-doublelist.o gsnap_avx512-bitvector.o gsnap_avx512-transcriptpool.o gsnap_avx512-exon.o gsnap_avx512-transcript.o gsnap_avx512-trpathpool.o gsnap_avx512-trpath.o gsnap_avx512-trpath-solve.o gsnap_avx512-trpath-convert.o gsnap_avx512-trpath-eval.o gsnap_avx512-transcriptome-search.o gsnap_avx512-vectorpool.o gsnap_avx512-repair.o gsnap_avx512-transcript-remap.o gsnap_avx512-transcript-velocity.o gsnap_avx512-intersect-small.o gsnap_avx512-intersect-uint2.o gsnap_avx512-intersect-approx-uint4.o gsnap_avx512-intersect-approx-indices-uint4.o gsnap_avx512-intersect-wdups-indices.o gsnap_avx512-intersect-lower-small.o gsnap_avx512-intersect-higher-small.o gsnap_avx512-intersect-indices-small.o gsnap_avx512-intersect-indices2-small.o gsnap_avx512-intersect-concordance-uint4.o gsnap_avx512-kmer-search.o gsnap_avx512-extension-search.o gsnap_avx512-repetitive.o gsnap_avx512-uint8table.o gsnap_avx512-uinttable.o gsnap_avx512-stage1hr.o gsnap_avx512-stage1hr-single.o gsnap_avx512-stage1hr-paired.o gsnap_avx512-uinttableuint.o gsnap_avx512-tableuint.o gsnap_avx512-single-cell.o gsnap_avx512-request.o gsnap_avx512-resulthr.o gsnap_avx512-output.o gsnap_avx512-inbuffer.o gsnap_avx512-samheader.o gsnap_avx512-printbuffer.o gsnap_avx512-outbuffer.o gsnap_avx512-uintpairtable.o gsnap_avx512-splice-count.o gsnap_avx512-support.o gsnap_avx512-datadir.o gsnap_avx512-parserange.o gsnap_avx512-getline.o gsnap_avx512-gsnap.o -lz -lbz2 -lm ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx512 gmapl_avx512-except.o gmapl_avx512-assert.o gmapl_avx512-mem.o gmapl_avx512-intlist.o gmapl_avx512-uintlist.o gmapl_avx512-uint8list.o gmapl_avx512-list.o gmapl_avx512-littleendian.o gmapl_avx512-bigendian.o gmapl_avx512-univinterval.o gmapl_avx512-interval.o gmapl_avx512-stopwatch.o gmapl_avx512-semaphore.o gmapl_avx512-access.o gmapl_avx512-filestring.o gmapl_avx512-iit-read-univ.o gmapl_avx512-iit-read.o gmapl_avx512-md5.o gmapl_avx512-bzip2.o gmapl_avx512-fopen.o gmapl_avx512-sequence.o gmapl_avx512-reader.o gmapl_avx512-genomicpos.o gmapl_avx512-compress.o gmapl_avx512-compress-write.o gmapl_avx512-gbuffer.o gmapl_avx512-genome.o gmapl_avx512-popcount.o gmapl_avx512-dinucl_bits.o gmapl_avx512-genome_canonical.o gmapl_avx512-genome-write.o gmapl_avx512-bitpack64-read.o gmapl_avx512-bitpack64-readtwo.o gmapl_avx512-indexdb.o gmapl_avx512-oligo.o gmapl_avx512-block.o gmapl_avx512-chrom.o gmapl_avx512-segmentpos.o gmapl_avx512-chrnum.o gmapl_avx512-uinttable_rh.o gmapl_avx512-uint8table_rh.o gmapl_avx512-gregion.o gmapl_avx512-match.o gmapl_avx512-matchpool.o gmapl_avx512-diagnostic.o gmapl_avx512-stage1.o gmapl_avx512-diag.o gmapl_avx512-diagpool.o gmapl_avx512-cmet.o gmapl_avx512-atoi.o gmapl_avx512-orderstat.o gmapl_avx512-oligoindex_hr.o gmapl_avx512-intron.o gmapl_avx512-maxent.o gmapl_avx512-maxent_hr.o gmapl_avx512-pair.o gmapl_avx512-pairpool.o gmapl_avx512-cellpool.o gmapl_avx512-stage2.o gmapl_avx512-doublelist.o gmapl_avx512-smooth.o gmapl_avx512-splicestringpool.o gmapl_avx512-splicetrie_build.o gmapl_avx512-splicetrie.o gmapl_avx512-boyer-moore.o gmapl_avx512-dynprog.o gmapl_avx512-dynprog_simd.o gmapl_avx512-dynprog_single.o gmapl_avx512-dynprog_genome.o gmapl_avx512-dynprog_cdna.o gmapl_avx512-dynprog_end.o gmapl_avx512-translation.o gmapl_avx512-pbinom.o gmapl_avx512-changepoint.o gmapl_avx512-stage3.o gmapl_avx512-request.o gmapl_avx512-result.o gmapl_avx512-output.o gmapl_avx512-inbuffer.o gmapl_avx512-samheader.o gmapl_avx512-printbuffer.o gmapl_avx512-outbuffer.o gmapl_avx512-chimera.o gmapl_avx512-datadir.o gmapl_avx512-parserange.o gmapl_avx512-getline.o gmapl_avx512-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx512 gsnapl_avx512-except.o gsnapl_avx512-assert.o gsnapl_avx512-mem.o gsnapl_avx512-intlist.o gsnapl_avx512-uintlist.o gsnapl_avx512-uint8list.o gsnapl_avx512-list.o gsnapl_avx512-littleendian.o gsnapl_avx512-bigendian.o gsnapl_avx512-univinterval.o gsnapl_avx512-interval.o gsnapl_avx512-stopwatch.o gsnapl_avx512-semaphore.o gsnapl_avx512-access.o gsnapl_avx512-filestring.o gsnapl_avx512-iit-read-univ.o gsnapl_avx512-iit-read.o gsnapl_avx512-bzip2.o gsnapl_avx512-reader.o gsnapl_avx512-genomicpos.o gsnapl_avx512-compress.o gsnapl_avx512-genome.o gsnapl_avx512-transcriptome.o gsnapl_avx512-popcount.o gsnapl_avx512-genomebits.o gsnapl_avx512-genomebits_consec.o gsnapl_avx512-genomebits_count.o gsnapl_avx512-genomebits_kmer.o gsnapl_avx512-genomebits_indel.o gsnapl_avx512-genomebits_decode.o gsnapl_avx512-genomebits_mismatches.o gsnapl_avx512-genomebits_trim.o gsnapl_avx512-dinucl_bits.o gsnapl_avx512-genome_sites.o gsnapl_avx512-bitpack64-read.o gsnapl_avx512-bitpack64-readtwo.o gsnapl_avx512-mergeinfo.o gsnapl_avx512-merge-diagonals-heap-uint8.o gsnapl_avx512-merge-uint8.o gsnapl_avx512-merge-diagonals-simd-uint8.o gsnapl_avx512-merge-diagonals-heap-uint4.o gsnapl_avx512-merge-uint4.o gsnapl_avx512-merge-diagonals-simd-uint4.o gsnapl_avx512-indexdb.o gsnapl_avx512-localdb-read.o gsnapl_avx512-oligo.o gsnapl_avx512-chrnum.o gsnapl_avx512-maxent_hr.o gsnapl_avx512-mapq.o gsnapl_avx512-fopen.o gsnapl_avx512-shortread.o gsnapl_avx512-junction.o gsnapl_avx512-concordance.o gsnapl_avx512-simplepair.o gsnapl_avx512-orderstat.o gsnapl_avx512-intlistpool.o gsnapl_avx512-uintlistpool.o gsnapl_avx512-uint8listpool.o gsnapl_avx512-listpool.o gsnapl_avx512-hitlistpool.o gsnapl_avx512-pathpool.o gsnapl_avx512-auxinfopool.o gsnapl_avx512-pathstorepool.o gsnapl_avx512-intron.o gsnapl_avx512-gbuffer.o gsnapl_avx512-select64-common.o gsnapl_avx512-select64-ones.o gsnapl_avx512-select64-zeroes.o gsnapl_avx512-ef64.o gsnapl_avx512-nr-x.o gsnapl_avx512-knownsplicing.o gsnapl_avx512-knownindels.o gsnapl_avx512-splice.o gsnapl_avx512-indel.o gsnapl_avx512-spliceendsgen.o gsnapl_avx512-spliceends.o gsnapl_avx512-bitpack64-access.o gsnapl_avx512-trdiag.o gsnapl_avx512-trdiagpool.o gsnapl_avx512-tr-extension-search.o gsnapl_avx512-univdiag.o gsnapl_avx512-univdiagpool.o gsnapl_avx512-sedgesort.o gsnapl_avx512-auxinfo.o gsnapl_avx512-pathstore.o gsnapl_avx512-altsplice.o gsnapl_avx512-path.o gsnapl_avx512-pathpair.o gsnapl_avx512-path-solve.o gsnapl_avx512-path-fusion.o gsnapl_avx512-path-trim.o gsnapl_avx512-path-eval.o gsnapl_avx512-pathpair-eval.o gsnapl_avx512-path-print-alignment.o gsnapl_avx512-path-print-m8.o gsnapl_avx512-path-print-sam.o gsnapl_avx512-path-learn.o gsnapl_avx512-method.o gsnapl_avx512-doublelist.o gsnapl_avx512-bitvector.o gsnapl_avx512-transcriptpool.o gsnapl_avx512-exon.o gsnapl_avx512-transcript.o gsnapl_avx512-trpathpool.o gsnapl_avx512-trpath.o gsnapl_avx512-trpath-solve.o gsnapl_avx512-trpath-convert.o gsnapl_avx512-trpath-eval.o gsnapl_avx512-transcriptome-search.o gsnapl_avx512-vectorpool.o gsnapl_avx512-repair.o gsnapl_avx512-transcript-remap.o gsnapl_avx512-transcript-velocity.o gsnapl_avx512-intersect-large.o gsnapl_avx512-intersect-small.o gsnapl_avx512-intersect-uint2.o gsnapl_avx512-intersect-approx-uint4.o gsnapl_avx512-intersect-approx-uint8.o gsnapl_avx512-intersect-approx-indices-uint8.o gsnapl_avx512-intersect-wdups-indices.o gsnapl_avx512-intersect-lower-large.o gsnapl_avx512-intersect-higher-large.o gsnapl_avx512-intersect-indices-small.o gsnapl_avx512-intersect-indices2-large.o gsnapl_avx512-intersect-indices-uint8.o gsnapl_avx512-intersect-concordance-uint8.o gsnapl_avx512-kmer-search.o gsnapl_avx512-extension-search.o gsnapl_avx512-repetitive.o gsnapl_avx512-uint8table.o gsnapl_avx512-stage1hr.o gsnapl_avx512-stage1hr-single.o gsnapl_avx512-stage1hr-paired.o gsnapl_avx512-uint8tableuint.o gsnapl_avx512-tableuint.o gsnapl_avx512-single-cell.o gsnapl_avx512-request.o gsnapl_avx512-resulthr.o gsnapl_avx512-output.o gsnapl_avx512-inbuffer.o gsnapl_avx512-samheader.o gsnapl_avx512-printbuffer.o gsnapl_avx512-outbuffer.o gsnapl_avx512-uint8pairtable.o gsnapl_avx512-splice-count.o gsnapl_avx512-support.o gsnapl_avx512-datadir.o gsnapl_avx512-parserange.o gsnapl_avx512-getline.o gsnapl_avx512-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build chmod +x gmap_process chmod +x gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords chmod +x gmap_cat chmod +x md_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites chmod +x psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x psl_introns chmod +x psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x ensembl_genes chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_introns cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites chmod +x gff3_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_genes cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x dbsnp_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_test --no-parallel cd build && make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making check in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' Making check in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making check in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make check-TESTS make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[5]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' PASS: align.test PASS: coords1.test PASS: setup1.test PASS: iit.test ============================================================================ Testsuite summary for gmap 2024-11-20 ============================================================================ # TOTAL: 4 # PASS: 4 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--builddir=build dh_prep -O--builddir=build debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' mkdir -p /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Genomic Mapping and Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gmap |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Genomic Short-read Nucleotide Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gsnap |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gsnap.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Large Genome Mapping and Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gmapl |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmapl.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Large Genome Short-read Nucleotide Alignment Program' \ /build/reproducible-path/gmap-2024-11-20+ds/build/src/gsnapl |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gsnapl.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Tool for genome database creation for GMAP or GSNAP' \ /build/reproducible-path/gmap-2024-11-20+ds/build/util/gmap_build |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap_build.1 dh_auto_install --builddir build_avx512 cd build_avx512 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx512 gmapl.avx512 gsnap.avx512 gsnapl.avx512 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[4]: Nothing to be done for 'install-exec-am'. /bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' dh_auto_install --builddir build_avx2 cd build_avx2 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx2 gmapl.avx2 gsnap.avx2 gsnapl.avx2 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[4]: Nothing to be done for 'install-exec-am'. /bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' dh_auto_install --builddir build_sse42 cd build_sse42 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse42 gmapl.sse42 gsnap.sse42 gsnapl.sse42 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[4]: Nothing to be done for 'install-exec-am'. /bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' dh_auto_install --builddir build_sse41 cd build_sse41 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse41 gmapl.sse41 gsnap.sse41 gsnapl.sse41 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[4]: Nothing to be done for 'install-exec-am'. /bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' dh_auto_install --builddir build_ssse3 cd build_ssse3 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.ssse3 gmapl.ssse3 gsnap.ssse3 gsnapl.ssse3 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[4]: Nothing to be done for 'install-exec-am'. /bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' dh_auto_install cd build && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse2 gmapl.sse2 gsnap.sse2 gsnapl.sse2 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making install in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[4]: Nothing to be done for 'install-exec-am'. /bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' mkdir -p debian/gmap/usr/bin dh_install for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \ cd /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap/; \ ls -1 gmap*.* gsnap*.* `; do \ ln -s /usr/lib/gmap/$bin debian/gmap/usr/bin/$bin; \ done make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_installdocs -O--builddir=build dh_installchangelogs -O--builddir=build debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' mkdir /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/doc/gmap/examples find tests/ -type f -print0 | xargs -0r sed -i \ -e 's@/build/reproducible-path/gmap-2024-11-20+ds@«buildpath»@g' \ -e 's@\#! /bin/bash@\#! /bin/sh@g' tar --sort=name \ --mtime="@1740521462" \ --owner=root --group=root --numeric-owner \ --mode=go=rX,u+rw,a-s \ --exclude='*/align.log' \ --exclude='*/Makefile' \ --exclude='*/Makefile.in' \ -cJf /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/doc/gmap/examples/tests.tar.xz tests make[1]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_installman -O--builddir=build dh_installsystemduser -O--builddir=build dh_lintian -O--builddir=build dh_perl -O--builddir=build dh_link -O--builddir=build dh_strip_nondeterminism -O--builddir=build dh_compress -O--builddir=build dh_fixperms -O--builddir=build dh_missing -O--builddir=build dh_dwz -a -O--builddir=build dh_strip -a -O--builddir=build dh_makeshlibs -a -O--builddir=build dh_shlibdeps -a -O--builddir=build dh_installdeb -O--builddir=build dh_gencontrol -O--builddir=build dh_md5sums -O--builddir=build dh_builddeb -O--builddir=build dpkg-deb: building package 'gmap' in '../gmap_2024-11-20+ds-2_amd64.deb'. dpkg-deb: building package 'gmap-dbgsym' in '../gmap-dbgsym_2024-11-20+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gmap_2024-11-20+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gmap_2024-11-20+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/301612/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/301612/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/301612 and its subdirectories I: Current time: Fri Sep 19 05:27:01 +14 2025 I: pbuilder-time-stamp: 1758209221 + false + set +x Thu Sep 18 15:27:01 UTC 2025 I: Signing ./b2/gmap_2024-11-20+ds-2_amd64.buildinfo as gmap_2024-11-20+ds-2_amd64.buildinfo.asc Thu Sep 18 15:27:01 UTC 2025 I: Signed ./b2/gmap_2024-11-20+ds-2_amd64.buildinfo as ./b2/gmap_2024-11-20+ds-2_amd64.buildinfo.asc Thu Sep 18 15:27:01 UTC 2025 - build #2 for gmap/forky/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Thu Sep 18 15:27:01 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-rVToKoE0, removing. /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI: total 7984 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 14:58 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 15:27 b2 -rw-rw-r-- 1 jenkins jenkins 2309 Feb 25 2025 gmap_2024-11-20+ds-2.dsc -rw------- 1 jenkins jenkins 8147027 Sep 18 14:58 rbuildlog.1Yuep4q /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b1: total 98152 -rw-r--r-- 1 jenkins jenkins 8143318 Sep 18 14:58 build.log -rw-r--r-- 1 jenkins jenkins 55899988 Sep 18 14:58 gmap-dbgsym_2024-11-20+ds-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 14076 Sep 18 14:58 gmap_2024-11-20+ds-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2309 Sep 18 14:58 gmap_2024-11-20+ds-2.dsc -rw-r--r-- 1 jenkins jenkins 5090 Sep 18 14:58 gmap_2024-11-20+ds-2_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5972 Sep 18 14:58 gmap_2024-11-20+ds-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1509 Sep 18 14:58 gmap_2024-11-20+ds-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 36295460 Sep 18 14:58 gmap_2024-11-20+ds-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1352 Sep 18 14:58 gmap_2024-11-20+ds-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b2: total 98040 -rw-rw-r-- 1 jenkins jenkins 8145220 Sep 18 15:27 build.log -rw-r--r-- 1 jenkins jenkins 55899988 Sep 18 15:27 gmap-dbgsym_2024-11-20+ds-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 14076 Sep 18 15:27 gmap_2024-11-20+ds-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2309 Sep 18 15:27 gmap_2024-11-20+ds-2.dsc -rw-rw-r-- 1 jenkins jenkins 5090 Sep 18 15:27 gmap_2024-11-20+ds-2_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5972 Sep 18 15:27 gmap_2024-11-20+ds-2_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1509 Sep 18 15:27 gmap_2024-11-20+ds-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 36295460 Sep 18 15:27 gmap_2024-11-20+ds-2_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1352 Sep 18 15:27 gmap_2024-11-20+ds-2_source.changes Thu Sep 18 15:27:02 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu Sep 18 15:27:03 UTC 2025 I: gmap_2024-11-20+ds-2_amd64.changes: Format: 1.8 Date: Tue, 25 Feb 2025 23:11:02 +0100 Source: gmap Binary: gmap gmap-dbgsym Architecture: amd64 Version: 2024-11-20+ds-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Closes: 1096727 Changes: gmap (2024-11-20+ds-2) unstable; urgency=medium . * c23.patch: new: fix build failure with gcc 15. (Closes: #1096727) * d/control: declare compliance to standards version 4.7.1. Checksums-Sha1: 48dd1b5cb0e53a8e5f45df9f83f1968b7fe8c3dd 55899988 gmap-dbgsym_2024-11-20+ds-2_amd64.deb 443f5457623a014190828413c3dd858ec768251c 5090 gmap_2024-11-20+ds-2_amd64.buildinfo a5f9ae9ed0fce3a748f41b179d63d5590d5080ca 36295460 gmap_2024-11-20+ds-2_amd64.deb Checksums-Sha256: 651bfbbe4d3cf111fdaf24906ef2b441526dd20ac64dbe649721f686d4515b05 55899988 gmap-dbgsym_2024-11-20+ds-2_amd64.deb 2c539ccfa73a31893bd8681545f67abbb1713f001f0f5746fe1bde6a451f2cd6 5090 gmap_2024-11-20+ds-2_amd64.buildinfo 99b603cadd0dfaa856b121b39245646cf681cae7af5f503e9b2ac3765570bbe3 36295460 gmap_2024-11-20+ds-2_amd64.deb Files: ab643e746f0b2fd51da59518380fa696 55899988 debug optional gmap-dbgsym_2024-11-20+ds-2_amd64.deb 36c99f6256f5ada8975760fe9464ad8b 5090 science optional gmap_2024-11-20+ds-2_amd64.buildinfo 94baab352ec599756337e708563888f7 36295460 science optional gmap_2024-11-20+ds-2_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/gmap_2024-11-20+ds-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/gmap_2024-11-20+ds-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/gmap_2024-11-20+ds-2.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/gmap_2024-11-20+ds-2.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/forky/amd64/gmap_2024-11-20+ds-2_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/gmap_2024-11-20+ds-2.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-18 14:58:56.908940551 +0000 +++ b2/build.log 2025-09-18 15:27:02.279040708 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Oct 21 09:10:58 -12 2026 -I: pbuilder-time-stamp: 1792617058 +I: Current time: Fri Sep 19 04:59:00 +14 2025 +I: pbuilder-time-stamp: 1758207540 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying c23.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2740700/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/301612/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 18 14:59 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/301612/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/301612/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d85274bf58c74458a9c9761240c5f1a7' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2740700' - PS1='# ' - PS2='> ' + INVOCATION_ID=879b9d08eb174724a59d21b116af9e25 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=301612 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/pbuilderrc_sc0r --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b1 --logfile b1/build.log gmap_2024-11-20+ds-2.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/pbuilderrc_xaTA --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b2 --logfile b2/build.log gmap_2024-11-20+ds-2.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2740700/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/301612/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -156,7 +188,7 @@ Get: 33 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 12.9 MB in 0s (121 MB/s) +Fetched 12.9 MB in 1s (12.7 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -311,7 +343,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gmap-2024-11-20+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gmap_2024-11-20+ds-2_source.changes +I: user script /srv/workspace/pbuilder/301612/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/301612/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gmap-2024-11-20+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gmap_2024-11-20+ds-2_source.changes dpkg-buildpackage: info: source package gmap dpkg-buildpackage: info: source version 2024-11-20+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -1806,7 +1842,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds' dh_auto_build - cd build && make -j42 + cd build && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' @@ -1849,10 +1885,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -1872,7 +1904,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -1893,6 +1927,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -1918,11 +1954,8 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1947,6 +1980,23 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -2075,6 +2125,7 @@ 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2186,10 +2237,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c @@ -2199,18 +2246,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c @@ -2218,6 +2254,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -2243,6 +2285,7 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -2268,28 +2311,54 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~ + | | + | Oligospace_T {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ +../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu +../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~~~~~~~~~~~~ + | | + | UINT8 {aka long unsigned int} +../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] + 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~ + | | + | UINT8 {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2308,6 +2377,16 @@ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ +../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); + | ~~~~~~~~~ + | | + | Oligospace_T {aka long unsigned int} ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2358,235 +2437,14 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': -../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~ - | | - | Oligospace_T {aka long unsigned int} -../../src/bitpack64-write.c:5396:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu -../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~~~~~~~~~~~~ - | | - | UINT8 {aka long unsigned int} -../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] - 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~ - | | - | UINT8 {aka long unsigned int} -../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); - | ~~~~~~~~~ - | | - | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/compress-write.c: In function 'put_compressed_one': ../../src/bitpack64-write.c:5424:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -2617,12 +2475,33 @@ | ~ | | | Oligospace_T {aka long unsigned int} +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -2643,17 +2522,8 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/compress-write.c: In function 'Compress_compress': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -2681,6 +2551,12 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -2763,27 +2639,157 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro 'FREAD_UINT' 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro 'FREAD_UINTS' 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2791,6 +2797,14 @@ 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp': +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2809,6 +2823,10 @@ ../../src/sarray-write.c:1064:5: note: in expansion of macro 'FREAD_UINTS' 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2839,6 +2857,12 @@ ../../src/sarray-write.c:1141:5: note: in expansion of macro 'FREAD_UINT' 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) @@ -2888,6 +2912,19 @@ ../../src/sarray-write.c:1371:5: note: in expansion of macro 'FREAD_UINT' 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -2907,22 +2944,10 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -2942,6 +2967,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -2962,6 +2988,18 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -3012,8 +3050,115 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3083,7 +3228,6 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -3104,12 +3248,9 @@ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -3124,22 +3265,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -3177,6 +3306,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -3249,13 +3379,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -3263,7 +3387,13 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -3290,13 +3420,6 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -3379,6 +3502,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -3390,6 +3514,24 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3398,117 +3540,37 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +../../src/indexdb-cat.c: In function 'main': +../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | | Univcoord_T {aka long unsigned int} + | long long unsigned int + | %lu +../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); + | ~~~^ ~~~~~~~~~~~~~~~~~~ + | | | + | | Univcoord_T {aka long unsigned int} + | long long unsigned int + | %lu ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -3528,25 +3590,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/indexdb-cat.c: In function 'main': -../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -../../src/indexdb-cat.c:827:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -3559,37 +3606,18 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | | Univcoord_T {aka long unsigned int} - | long long unsigned int - | %lu -../../src/indexdb-cat.c:901:19: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); - | ~~~^ ~~~~~~~~~~~~~~~~~~ - | | | - | | Univcoord_T {aka long unsigned int} - | long long unsigned int - | %lu ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -3640,37 +3668,17 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); @@ -3679,8 +3687,11 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -3700,15 +3711,32 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -3759,9 +3787,39 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -3880,29 +3938,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3988,7 +4023,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -4009,19 +4043,13 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -4047,7 +4075,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -4073,7 +4100,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4173,62 +4207,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4237,7 +4215,9 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/iit-read.c: In function 'IIT_read': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4290,13 +4270,13 @@ ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4315,8 +4295,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -4325,6 +4304,7 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4337,9 +4317,77 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +../../src/bigendian.c: In function 'Bigendian_write_char': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -4366,12 +4414,15 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4390,31 +4441,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4447,7 +4480,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -4515,8 +4547,113 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -4735,24 +4872,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -4767,48 +4887,7 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -4820,62 +4899,30 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c @@ -4902,23 +4949,11 @@ | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -4934,13 +4969,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -4966,7 +4996,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -4992,9 +5021,12 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -5002,6 +5034,7 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); @@ -5017,110 +5050,9 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5134,7 +5066,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -5225,6 +5156,110 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -5298,7 +5333,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -5444,11 +5478,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -../../src/indexdb.c: In function 'positions_read_multiple': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -5456,9 +5486,6 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -5477,6 +5504,15 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c @@ -5484,7 +5520,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -5496,6 +5531,7 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -5505,8 +5541,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -5520,14 +5554,13 @@ 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -5547,11 +5580,9 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -5602,10 +5633,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -5620,7 +5654,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5629,8 +5662,7 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5730,7 +5762,115 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -5804,7 +5944,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -5950,117 +6089,8 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -6075,7 +6105,6 @@ | | | | long long unsigned int long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -6087,18 +6116,17 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -6110,11 +6138,16 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -6134,6 +6167,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': @@ -6152,11 +6188,11 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c @@ -6188,6 +6224,7 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -6213,11 +6250,212 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -6436,215 +6674,10 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -6659,6 +6692,9 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -6668,12 +6704,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -6713,8 +6743,16 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -6765,17 +6803,122 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6873,9 +7016,12 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -6884,122 +7030,7 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -7011,10 +7042,15 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c @@ -7054,13 +7090,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -7068,6 +7097,13 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -7076,25 +7112,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': @@ -7117,6 +7134,25 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -7124,9 +7160,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -7177,11 +7210,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7274,7 +7306,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -7282,25 +7313,11 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7309,14 +7326,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -7324,7 +7333,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -7415,8 +7423,34 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -7428,9 +7462,13 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -7438,8 +7476,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c @@ -7481,9 +7517,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -7491,6 +7524,9 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c @@ -7501,7 +7537,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -7521,6 +7556,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c @@ -7540,19 +7576,13 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -7603,11 +7633,119 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7707,8 +7845,10 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7723,114 +7863,10 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c @@ -7844,12 +7880,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c @@ -7899,14 +7935,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c @@ -7921,6 +7949,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c @@ -7951,6 +7987,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -7958,9 +7996,8 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -7981,7 +8018,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -8016,7 +8052,6 @@ 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -8032,16 +8067,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -8092,14 +8123,67 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -8120,9 +8204,46 @@ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -8136,6 +8257,13 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -8149,6 +8277,15 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -8177,46 +8314,20 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read.c: In function 'IIT_debug': -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -8224,87 +8335,26 @@ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c @@ -8315,20 +8365,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c @@ -8337,6 +8373,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -8344,9 +8383,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c @@ -8377,6 +8413,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -8385,7 +8422,6 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c @@ -8394,30 +8430,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -8445,6 +8465,30 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c @@ -8459,14 +8503,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c @@ -8493,24 +8529,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -8558,7 +8576,19 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -8566,6 +8596,11 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -8591,21 +8626,41 @@ | | | unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -8620,11 +8675,12 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -8642,6 +8698,15 @@ 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -8692,135 +8757,9 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -8829,7 +8768,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -8866,7 +8804,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -8908,6 +8845,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -8928,19 +8866,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -8952,19 +8877,130 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c @@ -9010,9 +9046,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -9020,6 +9053,9 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c @@ -9027,8 +9063,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -9065,18 +9099,16 @@ 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -9127,6 +9159,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c @@ -9134,10 +9170,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -9168,7 +9202,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -9236,32 +9269,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -9367,14 +9375,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -../../src/indexdb.c: In function 'positions_read_multiple_large': -../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1897 | read(positions_high_fd,buffer,1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1901 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -9386,8 +9387,43 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +../../src/compress-write.c: In function 'put_compressed_one': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +../../src/indexdb.c: In function 'positions_read_multiple_large': +../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1897 | read(positions_high_fd,buffer,1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1901 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c @@ -9434,6 +9470,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -9441,7 +9478,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c @@ -9452,6 +9488,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -9471,13 +9508,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -9494,6 +9529,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -9501,6 +9537,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -9526,7 +9563,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -9553,117 +9589,14 @@ 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -9671,6 +9604,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -9738,6 +9672,7 @@ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -9761,11 +9696,111 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -9780,6 +9815,7 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c @@ -9824,6 +9860,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c @@ -9839,14 +9883,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c @@ -9904,8 +9940,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -9913,6 +9947,28 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -9923,7 +9979,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -9943,6 +9998,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -9963,35 +10021,17 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -10018,6 +10058,7 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -10042,16 +10083,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -10144,20 +10177,21 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c ../../src/iit-read-univ.c: In function 'read_words_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -10172,8 +10206,6 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -10259,7 +10291,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -10280,6 +10312,10 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c @@ -10294,7 +10330,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -10302,6 +10337,7 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c @@ -10325,7 +10361,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -10334,6 +10369,7 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c @@ -10348,30 +10384,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int ../../src/path.c: In function 'Path_print': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ @@ -10398,17 +10411,32 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c @@ -10432,6 +10460,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c @@ -10503,12 +10539,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -10516,6 +10546,12 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm @@ -10523,6 +10559,30 @@ gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -10536,6 +10596,7 @@ | | | unsigned int | %lu +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ @@ -10548,31 +10609,6 @@ | | | unsigned int | %lu -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm @@ -10581,8 +10617,8 @@ gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.sse2 gmap_sse2-except.o gmap_sse2-assert.o gmap_sse2-mem.o gmap_sse2-intlist.o gmap_sse2-uintlist.o gmap_sse2-list.o gmap_sse2-littleendian.o gmap_sse2-bigendian.o gmap_sse2-univinterval.o gmap_sse2-interval.o gmap_sse2-stopwatch.o gmap_sse2-semaphore.o gmap_sse2-access.o gmap_sse2-filestring.o gmap_sse2-iit-read-univ.o gmap_sse2-iit-read.o gmap_sse2-md5.o gmap_sse2-bzip2.o gmap_sse2-fopen.o gmap_sse2-sequence.o gmap_sse2-reader.o gmap_sse2-genomicpos.o gmap_sse2-compress.o gmap_sse2-compress-write.o gmap_sse2-gbuffer.o gmap_sse2-genome.o gmap_sse2-popcount.o gmap_sse2-dinucl_bits.o gmap_sse2-genome_canonical.o gmap_sse2-genome-write.o gmap_sse2-bitpack64-read.o gmap_sse2-bitpack64-readtwo.o gmap_sse2-indexdb.o gmap_sse2-oligo.o gmap_sse2-block.o gmap_sse2-chrom.o gmap_sse2-segmentpos.o gmap_sse2-chrnum.o gmap_sse2-uinttable_rh.o gmap_sse2-gregion.o gmap_sse2-match.o gmap_sse2-matchpool.o gmap_sse2-diagnostic.o gmap_sse2-stage1.o gmap_sse2-diag.o gmap_sse2-diagpool.o gmap_sse2-cmet.o gmap_sse2-atoi.o gmap_sse2-orderstat.o gmap_sse2-oligoindex_hr.o gmap_sse2-intron.o gmap_sse2-maxent.o gmap_sse2-maxent_hr.o gmap_sse2-pair.o gmap_sse2-pairpool.o gmap_sse2-cellpool.o gmap_sse2-stage2.o gmap_sse2-doublelist.o gmap_sse2-smooth.o gmap_sse2-splicestringpool.o gmap_sse2-splicetrie_build.o gmap_sse2-splicetrie.o gmap_sse2-boyer-moore.o gmap_sse2-dynprog.o gmap_sse2-dynprog_simd.o gmap_sse2-dynprog_single.o gmap_sse2-dynprog_genome.o gmap_sse2-dynprog_cdna.o gmap_sse2-dynprog_end.o gmap_sse2-translation.o gmap_sse2-pbinom.o gmap_sse2-changepoint.o gmap_sse2-stage3.o gmap_sse2-request.o gmap_sse2-result.o gmap_sse2-output.o gmap_sse2-inbuffer.o gmap_sse2-samheader.o gmap_sse2-printbuffer.o gmap_sse2-outbuffer.o gmap_sse2-chimera.o gmap_sse2-datadir.o gmap_sse2-parserange.o gmap_sse2-getline.o gmap_sse2-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.sse2 gmapl_sse2-except.o gmapl_sse2-assert.o gmapl_sse2-mem.o gmapl_sse2-intlist.o gmapl_sse2-uintlist.o gmapl_sse2-uint8list.o gmapl_sse2-list.o gmapl_sse2-littleendian.o gmapl_sse2-bigendian.o gmapl_sse2-univinterval.o gmapl_sse2-interval.o gmapl_sse2-stopwatch.o gmapl_sse2-semaphore.o gmapl_sse2-access.o gmapl_sse2-filestring.o gmapl_sse2-iit-read-univ.o gmapl_sse2-iit-read.o gmapl_sse2-md5.o gmapl_sse2-bzip2.o gmapl_sse2-fopen.o gmapl_sse2-sequence.o gmapl_sse2-reader.o gmapl_sse2-genomicpos.o gmapl_sse2-compress.o gmapl_sse2-compress-write.o gmapl_sse2-gbuffer.o gmapl_sse2-genome.o gmapl_sse2-popcount.o gmapl_sse2-dinucl_bits.o gmapl_sse2-genome_canonical.o gmapl_sse2-genome-write.o gmapl_sse2-bitpack64-read.o gmapl_sse2-bitpack64-readtwo.o gmapl_sse2-indexdb.o gmapl_sse2-oligo.o gmapl_sse2-block.o gmapl_sse2-chrom.o gmapl_sse2-segmentpos.o gmapl_sse2-chrnum.o gmapl_sse2-uinttable_rh.o gmapl_sse2-uint8table_rh.o gmapl_sse2-gregion.o gmapl_sse2-match.o gmapl_sse2-matchpool.o gmapl_sse2-diagnostic.o gmapl_sse2-stage1.o gmapl_sse2-diag.o gmapl_sse2-diagpool.o gmapl_sse2-cmet.o gmapl_sse2-atoi.o gmapl_sse2-orderstat.o gmapl_sse2-oligoindex_hr.o gmapl_sse2-intron.o gmapl_sse2-maxent.o gmapl_sse2-maxent_hr.o gmapl_sse2-pair.o gmapl_sse2-pairpool.o gmapl_sse2-cellpool.o gmapl_sse2-stage2.o gmapl_sse2-doublelist.o gmapl_sse2-smooth.o gmapl_sse2-splicestringpool.o gmapl_sse2-splicetrie_build.o gmapl_sse2-splicetrie.o gmapl_sse2-boyer-moore.o gmapl_sse2-dynprog.o gmapl_sse2-dynprog_simd.o gmapl_sse2-dynprog_single.o gmapl_sse2-dynprog_genome.o gmapl_sse2-dynprog_cdna.o gmapl_sse2-dynprog_end.o gmapl_sse2-translation.o gmapl_sse2-pbinom.o gmapl_sse2-changepoint.o gmapl_sse2-stage3.o gmapl_sse2-request.o gmapl_sse2-result.o gmapl_sse2-output.o gmapl_sse2-inbuffer.o gmapl_sse2-samheader.o gmapl_sse2-printbuffer.o gmapl_sse2-outbuffer.o gmapl_sse2-chimera.o gmapl_sse2-datadir.o gmapl_sse2-parserange.o gmapl_sse2-getline.o gmapl_sse2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.sse2 gsnap_sse2-except.o gsnap_sse2-assert.o gsnap_sse2-mem.o gsnap_sse2-intlist.o gsnap_sse2-uintlist.o gsnap_sse2-list.o gsnap_sse2-littleendian.o gsnap_sse2-bigendian.o gsnap_sse2-univinterval.o gsnap_sse2-interval.o gsnap_sse2-stopwatch.o gsnap_sse2-semaphore.o gsnap_sse2-access.o gsnap_sse2-filestring.o gsnap_sse2-iit-read-univ.o gsnap_sse2-iit-read.o gsnap_sse2-bzip2.o gsnap_sse2-reader.o gsnap_sse2-genomicpos.o gsnap_sse2-compress.o gsnap_sse2-genome.o gsnap_sse2-transcriptome.o gsnap_sse2-popcount.o gsnap_sse2-genomebits.o gsnap_sse2-genomebits_consec.o gsnap_sse2-genomebits_count.o gsnap_sse2-genomebits_kmer.o gsnap_sse2-genomebits_indel.o gsnap_sse2-genomebits_decode.o gsnap_sse2-genomebits_mismatches.o gsnap_sse2-genomebits_trim.o gsnap_sse2-dinucl_bits.o gsnap_sse2-genome_sites.o gsnap_sse2-bitpack64-read.o gsnap_sse2-bitpack64-readtwo.o gsnap_sse2-mergeinfo.o gsnap_sse2-merge-diagonals-heap-uint4.o gsnap_sse2-merge-uint4.o gsnap_sse2-merge-diagonals-simd-uint4.o gsnap_sse2-indexdb.o gsnap_sse2-localdb-read.o gsnap_sse2-oligo.o gsnap_sse2-chrnum.o gsnap_sse2-maxent_hr.o gsnap_sse2-mapq.o gsnap_sse2-fopen.o gsnap_sse2-shortread.o gsnap_sse2-junction.o gsnap_sse2-concordance.o gsnap_sse2-simplepair.o gsnap_sse2-orderstat.o gsnap_sse2-intlistpool.o gsnap_sse2-uintlistpool.o gsnap_sse2-listpool.o gsnap_sse2-hitlistpool.o gsnap_sse2-pathpool.o gsnap_sse2-auxinfopool.o gsnap_sse2-pathstorepool.o gsnap_sse2-intron.o gsnap_sse2-gbuffer.o gsnap_sse2-select64-common.o gsnap_sse2-select64-ones.o gsnap_sse2-select64-zeroes.o gsnap_sse2-ef64.o gsnap_sse2-nr-x.o gsnap_sse2-knownsplicing.o gsnap_sse2-knownindels.o gsnap_sse2-splice.o gsnap_sse2-indel.o gsnap_sse2-spliceendsgen.o gsnap_sse2-spliceends.o gsnap_sse2-bitpack64-access.o gsnap_sse2-trdiag.o gsnap_sse2-trdiagpool.o gsnap_sse2-tr-extension-search.o gsnap_sse2-univdiag.o gsnap_sse2-univdiagpool.o gsnap_sse2-sedgesort.o gsnap_sse2-auxinfo.o gsnap_sse2-pathstore.o gsnap_sse2-altsplice.o gsnap_sse2-path.o gsnap_sse2-pathpair.o gsnap_sse2-path-solve.o gsnap_sse2-path-fusion.o gsnap_sse2-path-trim.o gsnap_sse2-path-eval.o gsnap_sse2-pathpair-eval.o gsnap_sse2-path-print-alignment.o gsnap_sse2-path-print-m8.o gsnap_sse2-path-print-sam.o gsnap_sse2-path-learn.o gsnap_sse2-method.o gsnap_sse2-doublelist.o gsnap_sse2-bitvector.o gsnap_sse2-transcriptpool.o gsnap_sse2-exon.o gsnap_sse2-transcript.o gsnap_sse2-trpathpool.o gsnap_sse2-trpath.o gsnap_sse2-trpath-solve.o gsnap_sse2-trpath-convert.o gsnap_sse2-trpath-eval.o gsnap_sse2-transcriptome-search.o gsnap_sse2-vectorpool.o gsnap_sse2-repair.o gsnap_sse2-transcript-remap.o gsnap_sse2-transcript-velocity.o gsnap_sse2-intersect-small.o gsnap_sse2-intersect-uint2.o gsnap_sse2-intersect-approx-uint4.o gsnap_sse2-intersect-approx-indices-uint4.o gsnap_sse2-intersect-wdups-indices.o gsnap_sse2-intersect-lower-small.o gsnap_sse2-intersect-higher-small.o gsnap_sse2-intersect-indices-small.o gsnap_sse2-intersect-indices2-small.o gsnap_sse2-intersect-concordance-uint4.o gsnap_sse2-kmer-search.o gsnap_sse2-extension-search.o gsnap_sse2-repetitive.o gsnap_sse2-uint8table.o gsnap_sse2-uinttable.o gsnap_sse2-stage1hr.o gsnap_sse2-stage1hr-single.o gsnap_sse2-stage1hr-paired.o gsnap_sse2-uinttableuint.o gsnap_sse2-tableuint.o gsnap_sse2-single-cell.o gsnap_sse2-request.o gsnap_sse2-resulthr.o gsnap_sse2-output.o gsnap_sse2-inbuffer.o gsnap_sse2-samheader.o gsnap_sse2-printbuffer.o gsnap_sse2-outbuffer.o gsnap_sse2-uintpairtable.o gsnap_sse2-splice-count.o gsnap_sse2-support.o gsnap_sse2-datadir.o gsnap_sse2-parserange.o gsnap_sse2-getline.o gsnap_sse2-gsnap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.sse2 gmapl_sse2-except.o gmapl_sse2-assert.o gmapl_sse2-mem.o gmapl_sse2-intlist.o gmapl_sse2-uintlist.o gmapl_sse2-uint8list.o gmapl_sse2-list.o gmapl_sse2-littleendian.o gmapl_sse2-bigendian.o gmapl_sse2-univinterval.o gmapl_sse2-interval.o gmapl_sse2-stopwatch.o gmapl_sse2-semaphore.o gmapl_sse2-access.o gmapl_sse2-filestring.o gmapl_sse2-iit-read-univ.o gmapl_sse2-iit-read.o gmapl_sse2-md5.o gmapl_sse2-bzip2.o gmapl_sse2-fopen.o gmapl_sse2-sequence.o gmapl_sse2-reader.o gmapl_sse2-genomicpos.o gmapl_sse2-compress.o gmapl_sse2-compress-write.o gmapl_sse2-gbuffer.o gmapl_sse2-genome.o gmapl_sse2-popcount.o gmapl_sse2-dinucl_bits.o gmapl_sse2-genome_canonical.o gmapl_sse2-genome-write.o gmapl_sse2-bitpack64-read.o gmapl_sse2-bitpack64-readtwo.o gmapl_sse2-indexdb.o gmapl_sse2-oligo.o gmapl_sse2-block.o gmapl_sse2-chrom.o gmapl_sse2-segmentpos.o gmapl_sse2-chrnum.o gmapl_sse2-uinttable_rh.o gmapl_sse2-uint8table_rh.o gmapl_sse2-gregion.o gmapl_sse2-match.o gmapl_sse2-matchpool.o gmapl_sse2-diagnostic.o gmapl_sse2-stage1.o gmapl_sse2-diag.o gmapl_sse2-diagpool.o gmapl_sse2-cmet.o gmapl_sse2-atoi.o gmapl_sse2-orderstat.o gmapl_sse2-oligoindex_hr.o gmapl_sse2-intron.o gmapl_sse2-maxent.o gmapl_sse2-maxent_hr.o gmapl_sse2-pair.o gmapl_sse2-pairpool.o gmapl_sse2-cellpool.o gmapl_sse2-stage2.o gmapl_sse2-doublelist.o gmapl_sse2-smooth.o gmapl_sse2-splicestringpool.o gmapl_sse2-splicetrie_build.o gmapl_sse2-splicetrie.o gmapl_sse2-boyer-moore.o gmapl_sse2-dynprog.o gmapl_sse2-dynprog_simd.o gmapl_sse2-dynprog_single.o gmapl_sse2-dynprog_genome.o gmapl_sse2-dynprog_cdna.o gmapl_sse2-dynprog_end.o gmapl_sse2-translation.o gmapl_sse2-pbinom.o gmapl_sse2-changepoint.o gmapl_sse2-stage3.o gmapl_sse2-request.o gmapl_sse2-result.o gmapl_sse2-output.o gmapl_sse2-inbuffer.o gmapl_sse2-samheader.o gmapl_sse2-printbuffer.o gmapl_sse2-outbuffer.o gmapl_sse2-chimera.o gmapl_sse2-datadir.o gmapl_sse2-parserange.o gmapl_sse2-getline.o gmapl_sse2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.sse2 gsnapl_sse2-except.o gsnapl_sse2-assert.o gsnapl_sse2-mem.o gsnapl_sse2-intlist.o gsnapl_sse2-uintlist.o gsnapl_sse2-uint8list.o gsnapl_sse2-list.o gsnapl_sse2-littleendian.o gsnapl_sse2-bigendian.o gsnapl_sse2-univinterval.o gsnapl_sse2-interval.o gsnapl_sse2-stopwatch.o gsnapl_sse2-semaphore.o gsnapl_sse2-access.o gsnapl_sse2-filestring.o gsnapl_sse2-iit-read-univ.o gsnapl_sse2-iit-read.o gsnapl_sse2-bzip2.o gsnapl_sse2-reader.o gsnapl_sse2-genomicpos.o gsnapl_sse2-compress.o gsnapl_sse2-genome.o gsnapl_sse2-transcriptome.o gsnapl_sse2-popcount.o gsnapl_sse2-genomebits.o gsnapl_sse2-genomebits_consec.o gsnapl_sse2-genomebits_count.o gsnapl_sse2-genomebits_kmer.o gsnapl_sse2-genomebits_indel.o gsnapl_sse2-genomebits_decode.o gsnapl_sse2-genomebits_mismatches.o gsnapl_sse2-genomebits_trim.o gsnapl_sse2-dinucl_bits.o gsnapl_sse2-genome_sites.o gsnapl_sse2-bitpack64-read.o gsnapl_sse2-bitpack64-readtwo.o gsnapl_sse2-mergeinfo.o gsnapl_sse2-merge-diagonals-heap-uint8.o gsnapl_sse2-merge-uint8.o gsnapl_sse2-merge-diagonals-simd-uint8.o gsnapl_sse2-merge-diagonals-heap-uint4.o gsnapl_sse2-merge-uint4.o gsnapl_sse2-merge-diagonals-simd-uint4.o gsnapl_sse2-indexdb.o gsnapl_sse2-localdb-read.o gsnapl_sse2-oligo.o gsnapl_sse2-chrnum.o gsnapl_sse2-maxent_hr.o gsnapl_sse2-mapq.o gsnapl_sse2-fopen.o gsnapl_sse2-shortread.o gsnapl_sse2-junction.o gsnapl_sse2-concordance.o gsnapl_sse2-simplepair.o gsnapl_sse2-orderstat.o gsnapl_sse2-intlistpool.o gsnapl_sse2-uintlistpool.o gsnapl_sse2-uint8listpool.o gsnapl_sse2-listpool.o gsnapl_sse2-hitlistpool.o gsnapl_sse2-pathpool.o gsnapl_sse2-auxinfopool.o gsnapl_sse2-pathstorepool.o gsnapl_sse2-intron.o gsnapl_sse2-gbuffer.o gsnapl_sse2-select64-common.o gsnapl_sse2-select64-ones.o gsnapl_sse2-select64-zeroes.o gsnapl_sse2-ef64.o gsnapl_sse2-nr-x.o gsnapl_sse2-knownsplicing.o gsnapl_sse2-knownindels.o gsnapl_sse2-splice.o gsnapl_sse2-indel.o gsnapl_sse2-spliceendsgen.o gsnapl_sse2-spliceends.o gsnapl_sse2-bitpack64-access.o gsnapl_sse2-trdiag.o gsnapl_sse2-trdiagpool.o gsnapl_sse2-tr-extension-search.o gsnapl_sse2-univdiag.o gsnapl_sse2-univdiagpool.o gsnapl_sse2-sedgesort.o gsnapl_sse2-auxinfo.o gsnapl_sse2-pathstore.o gsnapl_sse2-altsplice.o gsnapl_sse2-path.o gsnapl_sse2-pathpair.o gsnapl_sse2-path-solve.o gsnapl_sse2-path-fusion.o gsnapl_sse2-path-trim.o gsnapl_sse2-path-eval.o gsnapl_sse2-pathpair-eval.o gsnapl_sse2-path-print-alignment.o gsnapl_sse2-path-print-m8.o gsnapl_sse2-path-print-sam.o gsnapl_sse2-path-learn.o gsnapl_sse2-method.o gsnapl_sse2-doublelist.o gsnapl_sse2-bitvector.o gsnapl_sse2-transcriptpool.o gsnapl_sse2-exon.o gsnapl_sse2-transcript.o gsnapl_sse2-trpathpool.o gsnapl_sse2-trpath.o gsnapl_sse2-trpath-solve.o gsnapl_sse2-trpath-convert.o gsnapl_sse2-trpath-eval.o gsnapl_sse2-transcriptome-search.o gsnapl_sse2-vectorpool.o gsnapl_sse2-repair.o gsnapl_sse2-transcript-remap.o gsnapl_sse2-transcript-velocity.o gsnapl_sse2-intersect-large.o gsnapl_sse2-intersect-small.o gsnapl_sse2-intersect-uint2.o gsnapl_sse2-intersect-approx-uint4.o gsnapl_sse2-intersect-approx-uint8.o gsnapl_sse2-intersect-approx-indices-uint8.o gsnapl_sse2-intersect-wdups-indices.o gsnapl_sse2-intersect-lower-large.o gsnapl_sse2-intersect-higher-large.o gsnapl_sse2-intersect-indices-small.o gsnapl_sse2-intersect-indices2-large.o gsnapl_sse2-intersect-indices-uint8.o gsnapl_sse2-intersect-concordance-uint8.o gsnapl_sse2-kmer-search.o gsnapl_sse2-extension-search.o gsnapl_sse2-repetitive.o gsnapl_sse2-uint8table.o gsnapl_sse2-stage1hr.o gsnapl_sse2-stage1hr-single.o gsnapl_sse2-stage1hr-paired.o gsnapl_sse2-uint8tableuint.o gsnapl_sse2-tableuint.o gsnapl_sse2-single-cell.o gsnapl_sse2-request.o gsnapl_sse2-resulthr.o gsnapl_sse2-output.o gsnapl_sse2-inbuffer.o gsnapl_sse2-samheader.o gsnapl_sse2-printbuffer.o gsnapl_sse2-outbuffer.o gsnapl_sse2-uint8pairtable.o gsnapl_sse2-splice-count.o gsnapl_sse2-support.o gsnapl_sse2-datadir.o gsnapl_sse2-parserange.o gsnapl_sse2-getline.o gsnapl_sse2-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' @@ -10596,35 +10632,35 @@ chmod +x gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords +chmod +x md_coords +chmod +x fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes -cp ensembl_genes.pl ensembl_genes -chmod +x md_coords -chmod +x fa_coords chmod +x psl_splicesites chmod +x psl_introns chmod +x psl_genes -chmod +x ensembl_genes +cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites +chmod +x ensembl_genes cp gtf_introns.pl gtf_introns -cp gtf_genes.pl gtf_genes chmod +x gtf_splicesites -cp gtf_transcript_splicesites.pl gtf_transcript_splicesites +cp gtf_genes.pl gtf_genes chmod +x gtf_introns chmod +x gtf_genes -chmod +x gtf_transcript_splicesites +cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites -cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites +cp gff3_introns.pl gff3_introns +chmod +x gtf_transcript_splicesites cp gff3_genes.pl gff3_genes -cp dbsnp_iit.pl dbsnp_iit -cp gvf_iit.pl gvf_iit chmod +x gff3_introns chmod +x gff3_genes +cp dbsnp_iit.pl dbsnp_iit +cp gvf_iit.pl gvf_iit chmod +x dbsnp_iit -cp vcf_iit.pl vcf_iit chmod +x gvf_iit +cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' Making all in tests @@ -10636,7 +10672,7 @@ make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' dh_auto_build --builddir build_ssse3 - cd build_ssse3 && make -j42 + cd build_ssse3 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' @@ -10682,18 +10718,57 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/bigendian.c: In function 'Bigendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); @@ -10709,6 +10784,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -10722,105 +10801,12 @@ 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -10846,7 +10832,6 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -10871,62 +10856,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -10977,18 +10910,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -11066,6 +10988,7 @@ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -11082,20 +11005,31 @@ 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -11109,7 +11043,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -11180,21 +11113,113 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -11208,13 +11233,23 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -11223,23 +11258,8 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -11248,7 +11268,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -11256,6 +11276,100 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -11283,6 +11397,7 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -11303,36 +11418,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -11349,6 +11434,7 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c:5424:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -11359,7 +11445,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -11433,18 +11518,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -11455,34 +11528,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -11519,8 +11564,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -11547,12 +11590,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -11560,19 +11598,6 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -11580,7 +11605,6 @@ | | | | long long unsigned int long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -11596,16 +11620,18 @@ ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -11743,8 +11769,19 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -11758,16 +11795,19 @@ 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -11784,15 +11824,10 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -11819,6 +11854,7 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -11852,7 +11888,107 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -11926,6 +12062,8 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -11999,14 +12137,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -12023,12 +12153,6 @@ | | | long long unsigned int | %lu -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -12039,12 +12163,6 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5603:87: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -12055,19 +12173,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -12078,6 +12183,12 @@ | ~ | | | Oligospace_T {aka long unsigned int} +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -12104,83 +12215,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -12277,12 +12312,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -12297,6 +12326,10 @@ | | | | long long unsigned int long unsigned int | %lu +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -12305,12 +12338,6 @@ | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -12322,6 +12349,13 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -12330,11 +12364,14 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); @@ -12348,7 +12385,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/indexdb-cat.c:901:14: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ @@ -12365,7 +12401,14 @@ | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -12384,13 +12427,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -12399,7 +12435,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -12408,6 +12443,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c @@ -12417,6 +12453,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -12467,9 +12506,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -12478,6 +12514,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); @@ -12486,12 +12523,10 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); @@ -12507,6 +12542,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -12534,13 +12570,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/access.c: In function 'copy_memory_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -12565,7 +12595,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -12591,8 +12620,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -12669,6 +12703,25 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -12692,59 +12745,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -12753,33 +12753,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -12787,31 +12760,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -12854,8 +12802,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -12884,6 +12830,8 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -12891,8 +12839,18 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -12905,9 +12863,74 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -13007,56 +13030,21 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -13143,7 +13131,6 @@ 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -13163,12 +13150,59 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -13191,6 +13225,7 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -13215,116 +13250,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -13339,7 +13265,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -13348,7 +13273,11 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -13419,7 +13348,6 @@ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -13449,8 +13377,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -13669,18 +13597,64 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -13688,6 +13662,49 @@ | | | | long long unsigned int long unsigned int | %lu +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -13700,6 +13717,25 @@ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -13707,20 +13743,26 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/bigendian.c: In function 'Bigendian_write_char': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -13735,6 +13777,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -13747,22 +13794,11 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -13770,7 +13806,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -13820,8 +13858,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read-univ.c:12: @@ -13900,7 +13936,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -13938,14 +13973,7 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -13954,6 +13982,14 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -13977,7 +14013,6 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -14052,9 +14087,8 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -14164,6 +14198,8 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -14273,10 +14309,8 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -14302,21 +14336,14 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +../../src/indexdb.c: In function 'positions_read_multiple': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -14328,13 +14355,42 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -14351,36 +14407,14 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -14431,10 +14465,9 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -14480,6 +14513,7 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -14528,25 +14562,25 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': +../../src/compress-write.c: In function 'put_compressed_one': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); @@ -14554,7 +14588,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -14563,8 +14596,6 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -14664,9 +14695,12 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14739,7 +14773,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -14885,13 +14919,14 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -14906,6 +14941,7 @@ | | | | long long unsigned int long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -14917,12 +14953,6 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -14934,6 +14964,12 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c @@ -14944,6 +14980,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -14963,13 +15001,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -14986,13 +15021,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -15043,8 +15077,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -15144,113 +15181,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -15469,10 +15399,120 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -15481,26 +15521,25 @@ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); @@ -15516,10 +15555,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -15540,13 +15577,14 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -15597,7 +15635,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -15697,18 +15742,16 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -15717,6 +15760,8 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -15724,18 +15769,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -15765,8 +15799,8 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/iit-read.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -15808,14 +15842,15 @@ 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/iit-read.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -15828,23 +15863,24 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c @@ -15886,6 +15922,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -15893,9 +15932,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -15906,6 +15942,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -15925,7 +15962,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -15946,19 +15983,9 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -16009,12 +16036,16 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -16091,7 +16122,7 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -16108,6 +16139,7 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -16115,6 +16147,10 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': @@ -16139,6 +16175,19 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -16196,7 +16245,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -16245,21 +16293,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -16267,6 +16301,8 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c @@ -16313,10 +16349,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -16324,6 +16356,10 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -16332,6 +16368,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -16351,8 +16388,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -16373,6 +16408,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -16382,10 +16418,81 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -16429,7 +16536,6 @@ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -16454,6 +16560,8 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -16461,7 +16569,12 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -16479,93 +16592,13 @@ 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -16602,6 +16635,7 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -16662,6 +16696,8 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c @@ -16675,11 +16711,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c @@ -16708,6 +16744,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c @@ -16723,14 +16767,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c @@ -16779,8 +16815,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -16788,6 +16822,8 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c @@ -16798,6 +16834,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -16807,7 +16846,6 @@ inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -16819,11 +16857,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -16843,6 +16876,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -16873,7 +16909,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -16924,11 +16959,108 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -17002,6 +17134,7 @@ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -17014,6 +17147,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -17034,107 +17168,13 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -17149,10 +17189,6 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c @@ -17166,6 +17202,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -17173,8 +17211,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c @@ -17205,8 +17241,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -17215,6 +17249,8 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c @@ -17224,14 +17260,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", @@ -17253,6 +17284,8 @@ | ~~~~~~~~~~~~~ | | | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -17280,11 +17313,6 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c @@ -17297,6 +17325,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c @@ -17327,11 +17363,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -17379,10 +17410,13 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -17390,16 +17424,35 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -17425,31 +17478,13 @@ | | | unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -17470,86 +17505,34 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -17649,6 +17632,59 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: @@ -17696,7 +17732,6 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -17710,6 +17745,7 @@ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -17745,7 +17781,6 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -17758,10 +17793,8 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -17773,27 +17806,30 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c @@ -17840,6 +17876,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -17847,7 +17884,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -17856,7 +17892,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -17876,9 +17911,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -17899,7 +17936,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -17909,6 +17945,57 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -18008,57 +18095,14 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -18067,7 +18111,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -18117,6 +18161,7 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/compress-write.c: In function 'put_compressed_one': ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -18145,6 +18190,19 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -18165,9 +18223,17 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -18179,38 +18245,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -18218,6 +18252,8 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c @@ -18263,9 +18299,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -18273,6 +18306,9 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -18282,8 +18318,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -18303,6 +18337,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -18331,6 +18367,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -18381,12 +18421,25 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -18464,7 +18517,6 @@ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -18487,6 +18539,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -18496,13 +18549,13 @@ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -18593,23 +18646,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c @@ -18626,11 +18662,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c @@ -18680,8 +18716,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -18690,6 +18724,8 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c @@ -18729,6 +18765,18 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -18738,6 +18786,7 @@ inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -18749,19 +18798,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -18774,29 +18810,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -18809,7 +18822,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -18818,73 +18830,39 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -18894,12 +18872,6 @@ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ @@ -18965,6 +18937,118 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -18988,22 +19072,6 @@ ../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -19023,7 +19091,6 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -19052,12 +19119,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -19078,31 +19139,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c @@ -19121,13 +19157,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c ../../src/indexdb.c: In function 'positions_read_multiple_large': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c @@ -19153,14 +19189,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -19169,10 +19197,46 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path.o `test -f 'path.c' || echo '../../src/'`path.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -19200,32 +19264,6 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -19234,8 +19272,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c @@ -19281,7 +19317,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -19329,23 +19364,10 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -19366,9 +19388,30 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -19394,20 +19437,13 @@ | | | unsigned int | %lu -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.ssse3 gmap_ssse3-except.o gmap_ssse3-assert.o gmap_ssse3-mem.o gmap_ssse3-intlist.o gmap_ssse3-uintlist.o gmap_ssse3-list.o gmap_ssse3-littleendian.o gmap_ssse3-bigendian.o gmap_ssse3-univinterval.o gmap_ssse3-interval.o gmap_ssse3-stopwatch.o gmap_ssse3-semaphore.o gmap_ssse3-access.o gmap_ssse3-filestring.o gmap_ssse3-iit-read-univ.o gmap_ssse3-iit-read.o gmap_ssse3-md5.o gmap_ssse3-bzip2.o gmap_ssse3-fopen.o gmap_ssse3-sequence.o gmap_ssse3-reader.o gmap_ssse3-genomicpos.o gmap_ssse3-compress.o gmap_ssse3-compress-write.o gmap_ssse3-gbuffer.o gmap_ssse3-genome.o gmap_ssse3-popcount.o gmap_ssse3-dinucl_bits.o gmap_ssse3-genome_canonical.o gmap_ssse3-genome-write.o gmap_ssse3-bitpack64-read.o gmap_ssse3-bitpack64-readtwo.o gmap_ssse3-indexdb.o gmap_ssse3-oligo.o gmap_ssse3-block.o gmap_ssse3-chrom.o gmap_ssse3-segmentpos.o gmap_ssse3-chrnum.o gmap_ssse3-uinttable_rh.o gmap_ssse3-gregion.o gmap_ssse3-match.o gmap_ssse3-matchpool.o gmap_ssse3-diagnostic.o gmap_ssse3-stage1.o gmap_ssse3-diag.o gmap_ssse3-diagpool.o gmap_ssse3-cmet.o gmap_ssse3-atoi.o gmap_ssse3-orderstat.o gmap_ssse3-oligoindex_hr.o gmap_ssse3-intron.o gmap_ssse3-maxent.o gmap_ssse3-maxent_hr.o gmap_ssse3-pair.o gmap_ssse3-pairpool.o gmap_ssse3-cellpool.o gmap_ssse3-stage2.o gmap_ssse3-doublelist.o gmap_ssse3-smooth.o gmap_ssse3-splicestringpool.o gmap_ssse3-splicetrie_build.o gmap_ssse3-splicetrie.o gmap_ssse3-boyer-moore.o gmap_ssse3-dynprog.o gmap_ssse3-dynprog_simd.o gmap_ssse3-dynprog_single.o gmap_ssse3-dynprog_genome.o gmap_ssse3-dynprog_cdna.o gmap_ssse3-dynprog_end.o gmap_ssse3-translation.o gmap_ssse3-pbinom.o gmap_ssse3-changepoint.o gmap_ssse3-stage3.o gmap_ssse3-request.o gmap_ssse3-result.o gmap_ssse3-output.o gmap_ssse3-inbuffer.o gmap_ssse3-samheader.o gmap_ssse3-printbuffer.o gmap_ssse3-outbuffer.o gmap_ssse3-chimera.o gmap_ssse3-datadir.o gmap_ssse3-parserange.o gmap_ssse3-getline.o gmap_ssse3-gmap.o -lz -lbz2 -lm @@ -19421,32 +19457,32 @@ cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat -cp md_coords.pl md_coords -chmod +x gmap_process chmod +x gmap_build +chmod +x gmap_process chmod +x gmap_cat +cp md_coords.pl md_coords cp fa_coords.pl fa_coords +chmod +x md_coords +chmod +x fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns -chmod +x fa_coords -chmod +x md_coords chmod +x psl_splicesites chmod +x psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes +chmod +x psl_genes +chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns -chmod +x psl_genes cp gtf_genes.pl gtf_genes -chmod +x ensembl_genes chmod +x gtf_splicesites chmod +x gtf_introns -cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes -chmod +x gtf_transcript_splicesites +cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites -cp gff3_introns.pl gff3_introns +chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites +cp gff3_introns.pl gff3_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_introns @@ -19466,7 +19502,7 @@ make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' dh_auto_build --builddir build_sse41 - cd build_sse41 && make -j42 + cd build_sse41 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' @@ -19498,16 +19534,31 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -19516,7 +19567,6 @@ ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); @@ -19528,14 +19578,27 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -19547,15 +19610,12 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -19574,25 +19634,212 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -19637,6 +19884,7 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -19685,7 +19933,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -19699,55 +19946,51 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -19780,6 +20023,7 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -19847,110 +20091,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -19988,6 +20130,14 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -20077,57 +20227,6 @@ | | | long long unsigned int | %lu -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -20184,6 +20283,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -20220,94 +20320,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -20361,6 +20374,10 @@ ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -20405,6 +20422,35 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -20416,7 +20462,12 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -20505,6 +20556,7 @@ ../../src/sarray-write.c:1288:5: note: in expansion of macro 'FREAD_UINTS' 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -20554,27 +20606,9 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -20594,7 +20628,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -20615,6 +20649,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c @@ -20623,6 +20659,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -20649,7 +20686,6 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -20676,8 +20712,6 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -20777,10 +20811,14 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -20789,110 +20827,8 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -20965,6 +20901,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/iit-read.c: In function 'IIT_read': ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -20975,6 +20912,12 @@ | ~ | | | Oligospace_T {aka long unsigned int} +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -21001,7 +20944,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -21039,6 +20981,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/iit-read.c: In function 'read_tree': ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -21111,21 +21054,102 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -21133,13 +21157,6 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -21151,7 +21168,20 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -21160,11 +21190,16 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); @@ -21192,9 +21227,11 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -21214,7 +21251,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -21235,17 +21276,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -21296,12 +21331,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); @@ -21310,19 +21344,13 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -21342,13 +21370,12 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -21364,9 +21391,16 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -21417,58 +21451,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/bigendian.c: In function 'Bigendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -21546,6 +21529,7 @@ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -21568,65 +21552,61 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': +../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -21634,6 +21614,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -21676,11 +21657,11 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -21725,20 +21706,70 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -21838,56 +21869,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -21896,58 +21877,8 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -../../src/access.c: In function 'copy_memory_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c: In function 'IIT_read': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -21970,7 +21901,6 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -22045,12 +21975,118 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +../../src/compress-write.c: In function 'put_compressed_one': In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -22084,8 +22120,6 @@ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -22123,6 +22157,12 @@ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -22145,28 +22185,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); @@ -22174,7 +22192,29 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -../../src/iit-read.c: In function 'IIT_read': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -22285,12 +22325,6 @@ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -22399,6 +22433,46 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -22442,14 +22516,6 @@ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -22477,6 +22543,10 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -22497,46 +22567,15 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -22548,10 +22587,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -22571,7 +22606,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -22592,10 +22627,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -22646,7 +22683,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c @@ -22655,6 +22691,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -22669,18 +22709,8 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -22711,12 +22741,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -22777,29 +22801,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -22807,86 +22808,14 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -23079,6 +23008,10 @@ | ~ | | | Oligospace_T {aka long unsigned int} +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -23105,20 +23038,22 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -23126,6 +23061,14 @@ | | | | long long unsigned int long unsigned int | %lu +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -23137,18 +23080,102 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -23160,11 +23187,24 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/littleendian.c: In function 'Littleendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -23183,14 +23223,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -23204,13 +23240,6 @@ 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -23261,6 +23290,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': @@ -23279,13 +23315,13 @@ | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -23389,53 +23425,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -23453,12 +23442,6 @@ | | | long long unsigned int | %lu -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -23479,12 +23462,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -23557,16 +23534,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -23594,9 +23561,6 @@ | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5574:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -23607,15 +23571,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -23626,18 +23581,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5603:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -23694,6 +23643,95 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -23714,9 +23752,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); @@ -23735,7 +23770,6 @@ | | | | long long unsigned int long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -23747,6 +23781,8 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -23772,8 +23808,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -23793,6 +23827,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -23801,7 +23840,6 @@ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -23814,13 +23852,13 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -23871,8 +23909,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -23888,6 +23928,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -23978,110 +24019,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -24202,7 +24139,6 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -24301,12 +24237,9 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -24319,6 +24252,109 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -24327,9 +24363,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -24369,12 +24402,17 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -24425,17 +24463,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -24535,9 +24562,27 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -24546,7 +24591,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -24555,14 +24599,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -24633,6 +24669,18 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -24653,19 +24701,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -24715,8 +24751,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -24724,6 +24758,8 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c @@ -24737,6 +24773,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -24756,13 +24793,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -24778,6 +24813,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -24785,6 +24821,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -24835,110 +24875,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -24973,18 +24911,6 @@ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ @@ -25048,7 +24974,99 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': ../../src/compress-write.c: In function 'put_compressed_one': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ @@ -25056,39 +25074,59 @@ | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function 'Compress_compress': +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -25096,8 +25134,6 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c @@ -25147,6 +25183,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -25154,7 +25191,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -25175,6 +25211,8 @@ ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); @@ -25182,7 +25220,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -25203,15 +25242,10 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -25262,8 +25296,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -25363,7 +25397,10 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -25379,7 +25416,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -25470,8 +25506,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -25486,6 +25520,8 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c @@ -25504,11 +25540,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c @@ -25542,6 +25578,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c @@ -25560,14 +25604,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c @@ -25611,6 +25647,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -25618,15 +25657,8 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -25639,6 +25671,7 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c In function 'fgets', inlined from 'input_oneline' at ../../src/single-cell.c:169:14, inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, @@ -25647,6 +25680,9 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c @@ -25674,8 +25710,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -25693,12 +25727,18 @@ 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -25749,124 +25789,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -25910,8 +25836,6 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -25952,18 +25876,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -25984,9 +25896,133 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c @@ -25996,19 +26032,19 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c @@ -26031,6 +26067,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -26039,10 +26079,6 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c @@ -26055,29 +26091,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -26105,14 +26118,29 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c @@ -26135,6 +26163,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c @@ -26161,11 +26197,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -26213,7 +26244,10 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -26221,11 +26255,19 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -26251,14 +26293,9 @@ | | | unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -26278,7 +26315,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -26319,12 +26357,120 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -26350,6 +26496,7 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -26375,22 +26522,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26465,7 +26603,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -26489,8 +26626,11 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -26499,122 +26639,8 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -26626,6 +26652,16 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c @@ -26667,6 +26703,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -26674,8 +26712,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -26687,7 +26723,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -26707,7 +26742,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -26719,84 +26753,31 @@ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26894,7 +26875,64 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -27000,8 +27038,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] @@ -27019,7 +27055,6 @@ | long long unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -27028,7 +27063,7 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -27047,6 +27082,7 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c @@ -27095,8 +27131,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -27104,6 +27138,8 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -27112,9 +27148,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -27134,6 +27167,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -27154,6 +27188,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -27161,68 +27197,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -27320,23 +27300,59 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -27369,7 +27385,6 @@ 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -27443,6 +27458,27 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c @@ -27453,11 +27489,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c @@ -27498,9 +27534,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path.o `test -f 'path.c' || echo '../../src/'`path.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -27509,6 +27542,9 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c @@ -27566,10 +27602,16 @@ ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -27590,12 +27632,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c @@ -27605,6 +27641,26 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -27625,38 +27681,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -27739,7 +27769,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -27807,15 +27836,24 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -27830,14 +27868,6 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -27935,6 +27965,12 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c @@ -27958,13 +27994,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c ../../src/indexdb.c: In function 'positions_read_multiple_large': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c @@ -27986,6 +28022,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -27994,7 +28031,6 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c @@ -28006,30 +28042,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -28057,10 +28070,31 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -28069,6 +28103,8 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c @@ -28108,6 +28144,15 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -28155,34 +28200,8 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -28190,11 +28209,7 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -28220,6 +28235,7 @@ | | | unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm @@ -28240,8 +28256,28 @@ gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse41 gmapl_sse41-except.o gmapl_sse41-assert.o gmapl_sse41-mem.o gmapl_sse41-intlist.o gmapl_sse41-uintlist.o gmapl_sse41-uint8list.o gmapl_sse41-list.o gmapl_sse41-littleendian.o gmapl_sse41-bigendian.o gmapl_sse41-univinterval.o gmapl_sse41-interval.o gmapl_sse41-stopwatch.o gmapl_sse41-semaphore.o gmapl_sse41-access.o gmapl_sse41-filestring.o gmapl_sse41-iit-read-univ.o gmapl_sse41-iit-read.o gmapl_sse41-md5.o gmapl_sse41-bzip2.o gmapl_sse41-fopen.o gmapl_sse41-sequence.o gmapl_sse41-reader.o gmapl_sse41-genomicpos.o gmapl_sse41-compress.o gmapl_sse41-compress-write.o gmapl_sse41-gbuffer.o gmapl_sse41-genome.o gmapl_sse41-popcount.o gmapl_sse41-dinucl_bits.o gmapl_sse41-genome_canonical.o gmapl_sse41-genome-write.o gmapl_sse41-bitpack64-read.o gmapl_sse41-bitpack64-readtwo.o gmapl_sse41-indexdb.o gmapl_sse41-oligo.o gmapl_sse41-block.o gmapl_sse41-chrom.o gmapl_sse41-segmentpos.o gmapl_sse41-chrnum.o gmapl_sse41-uinttable_rh.o gmapl_sse41-uint8table_rh.o gmapl_sse41-gregion.o gmapl_sse41-match.o gmapl_sse41-matchpool.o gmapl_sse41-diagnostic.o gmapl_sse41-stage1.o gmapl_sse41-diag.o gmapl_sse41-diagpool.o gmapl_sse41-cmet.o gmapl_sse41-atoi.o gmapl_sse41-orderstat.o gmapl_sse41-oligoindex_hr.o gmapl_sse41-intron.o gmapl_sse41-maxent.o gmapl_sse41-maxent_hr.o gmapl_sse41-pair.o gmapl_sse41-pairpool.o gmapl_sse41-cellpool.o gmapl_sse41-stage2.o gmapl_sse41-doublelist.o gmapl_sse41-smooth.o gmapl_sse41-splicestringpool.o gmapl_sse41-splicetrie_build.o gmapl_sse41-splicetrie.o gmapl_sse41-boyer-moore.o gmapl_sse41-dynprog.o gmapl_sse41-dynprog_simd.o gmapl_sse41-dynprog_single.o gmapl_sse41-dynprog_genome.o gmapl_sse41-dynprog_cdna.o gmapl_sse41-dynprog_end.o gmapl_sse41-translation.o gmapl_sse41-pbinom.o gmapl_sse41-changepoint.o gmapl_sse41-stage3.o gmapl_sse41-request.o gmapl_sse41-result.o gmapl_sse41-output.o gmapl_sse41-inbuffer.o gmapl_sse41-samheader.o gmapl_sse41-printbuffer.o gmapl_sse41-outbuffer.o gmapl_sse41-chimera.o gmapl_sse41-datadir.o gmapl_sse41-parserange.o gmapl_sse41-getline.o gmapl_sse41-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse41 gmap_sse41-except.o gmap_sse41-assert.o gmap_sse41-mem.o gmap_sse41-intlist.o gmap_sse41-uintlist.o gmap_sse41-list.o gmap_sse41-littleendian.o gmap_sse41-bigendian.o gmap_sse41-univinterval.o gmap_sse41-interval.o gmap_sse41-stopwatch.o gmap_sse41-semaphore.o gmap_sse41-access.o gmap_sse41-filestring.o gmap_sse41-iit-read-univ.o gmap_sse41-iit-read.o gmap_sse41-md5.o gmap_sse41-bzip2.o gmap_sse41-fopen.o gmap_sse41-sequence.o gmap_sse41-reader.o gmap_sse41-genomicpos.o gmap_sse41-compress.o gmap_sse41-compress-write.o gmap_sse41-gbuffer.o gmap_sse41-genome.o gmap_sse41-popcount.o gmap_sse41-dinucl_bits.o gmap_sse41-genome_canonical.o gmap_sse41-genome-write.o gmap_sse41-bitpack64-read.o gmap_sse41-bitpack64-readtwo.o gmap_sse41-indexdb.o gmap_sse41-oligo.o gmap_sse41-block.o gmap_sse41-chrom.o gmap_sse41-segmentpos.o gmap_sse41-chrnum.o gmap_sse41-uinttable_rh.o gmap_sse41-gregion.o gmap_sse41-match.o gmap_sse41-matchpool.o gmap_sse41-diagnostic.o gmap_sse41-stage1.o gmap_sse41-diag.o gmap_sse41-diagpool.o gmap_sse41-cmet.o gmap_sse41-atoi.o gmap_sse41-orderstat.o gmap_sse41-oligoindex_hr.o gmap_sse41-intron.o gmap_sse41-maxent.o gmap_sse41-maxent_hr.o gmap_sse41-pair.o gmap_sse41-pairpool.o gmap_sse41-cellpool.o gmap_sse41-stage2.o gmap_sse41-doublelist.o gmap_sse41-smooth.o gmap_sse41-splicestringpool.o gmap_sse41-splicetrie_build.o gmap_sse41-splicetrie.o gmap_sse41-boyer-moore.o gmap_sse41-dynprog.o gmap_sse41-dynprog_simd.o gmap_sse41-dynprog_single.o gmap_sse41-dynprog_genome.o gmap_sse41-dynprog_cdna.o gmap_sse41-dynprog_end.o gmap_sse41-translation.o gmap_sse41-pbinom.o gmap_sse41-changepoint.o gmap_sse41-stage3.o gmap_sse41-request.o gmap_sse41-result.o gmap_sse41-output.o gmap_sse41-inbuffer.o gmap_sse41-samheader.o gmap_sse41-printbuffer.o gmap_sse41-outbuffer.o gmap_sse41-chimera.o gmap_sse41-datadir.o gmap_sse41-parserange.o gmap_sse41-getline.o gmap_sse41-gmap.o -lz -lbz2 -lm +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse41 gmapl_sse41-except.o gmapl_sse41-assert.o gmapl_sse41-mem.o gmapl_sse41-intlist.o gmapl_sse41-uintlist.o gmapl_sse41-uint8list.o gmapl_sse41-list.o gmapl_sse41-littleendian.o gmapl_sse41-bigendian.o gmapl_sse41-univinterval.o gmapl_sse41-interval.o gmapl_sse41-stopwatch.o gmapl_sse41-semaphore.o gmapl_sse41-access.o gmapl_sse41-filestring.o gmapl_sse41-iit-read-univ.o gmapl_sse41-iit-read.o gmapl_sse41-md5.o gmapl_sse41-bzip2.o gmapl_sse41-fopen.o gmapl_sse41-sequence.o gmapl_sse41-reader.o gmapl_sse41-genomicpos.o gmapl_sse41-compress.o gmapl_sse41-compress-write.o gmapl_sse41-gbuffer.o gmapl_sse41-genome.o gmapl_sse41-popcount.o gmapl_sse41-dinucl_bits.o gmapl_sse41-genome_canonical.o gmapl_sse41-genome-write.o gmapl_sse41-bitpack64-read.o gmapl_sse41-bitpack64-readtwo.o gmapl_sse41-indexdb.o gmapl_sse41-oligo.o gmapl_sse41-block.o gmapl_sse41-chrom.o gmapl_sse41-segmentpos.o gmapl_sse41-chrnum.o gmapl_sse41-uinttable_rh.o gmapl_sse41-uint8table_rh.o gmapl_sse41-gregion.o gmapl_sse41-match.o gmapl_sse41-matchpool.o gmapl_sse41-diagnostic.o gmapl_sse41-stage1.o gmapl_sse41-diag.o gmapl_sse41-diagpool.o gmapl_sse41-cmet.o gmapl_sse41-atoi.o gmapl_sse41-orderstat.o gmapl_sse41-oligoindex_hr.o gmapl_sse41-intron.o gmapl_sse41-maxent.o gmapl_sse41-maxent_hr.o gmapl_sse41-pair.o gmapl_sse41-pairpool.o gmapl_sse41-cellpool.o gmapl_sse41-stage2.o gmapl_sse41-doublelist.o gmapl_sse41-smooth.o gmapl_sse41-splicestringpool.o gmapl_sse41-splicetrie_build.o gmapl_sse41-splicetrie.o gmapl_sse41-boyer-moore.o gmapl_sse41-dynprog.o gmapl_sse41-dynprog_simd.o gmapl_sse41-dynprog_single.o gmapl_sse41-dynprog_genome.o gmapl_sse41-dynprog_cdna.o gmapl_sse41-dynprog_end.o gmapl_sse41-translation.o gmapl_sse41-pbinom.o gmapl_sse41-changepoint.o gmapl_sse41-stage3.o gmapl_sse41-request.o gmapl_sse41-result.o gmapl_sse41-output.o gmapl_sse41-inbuffer.o gmapl_sse41-samheader.o gmapl_sse41-printbuffer.o gmapl_sse41-outbuffer.o gmapl_sse41-chimera.o gmapl_sse41-datadir.o gmapl_sse41-parserange.o gmapl_sse41-getline.o gmapl_sse41-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse41 gsnap_sse41-except.o gsnap_sse41-assert.o gsnap_sse41-mem.o gsnap_sse41-intlist.o gsnap_sse41-uintlist.o gsnap_sse41-list.o gsnap_sse41-littleendian.o gsnap_sse41-bigendian.o gsnap_sse41-univinterval.o gsnap_sse41-interval.o gsnap_sse41-stopwatch.o gsnap_sse41-semaphore.o gsnap_sse41-access.o gsnap_sse41-filestring.o gsnap_sse41-iit-read-univ.o gsnap_sse41-iit-read.o gsnap_sse41-bzip2.o gsnap_sse41-reader.o gsnap_sse41-genomicpos.o gsnap_sse41-compress.o gsnap_sse41-genome.o gsnap_sse41-transcriptome.o gsnap_sse41-popcount.o gsnap_sse41-genomebits.o gsnap_sse41-genomebits_consec.o gsnap_sse41-genomebits_count.o gsnap_sse41-genomebits_kmer.o gsnap_sse41-genomebits_indel.o gsnap_sse41-genomebits_decode.o gsnap_sse41-genomebits_mismatches.o gsnap_sse41-genomebits_trim.o gsnap_sse41-dinucl_bits.o gsnap_sse41-genome_sites.o gsnap_sse41-bitpack64-read.o gsnap_sse41-bitpack64-readtwo.o gsnap_sse41-mergeinfo.o gsnap_sse41-merge-diagonals-heap-uint4.o gsnap_sse41-merge-uint4.o gsnap_sse41-merge-diagonals-simd-uint4.o gsnap_sse41-indexdb.o gsnap_sse41-localdb-read.o gsnap_sse41-oligo.o gsnap_sse41-chrnum.o gsnap_sse41-maxent_hr.o gsnap_sse41-mapq.o gsnap_sse41-fopen.o gsnap_sse41-shortread.o gsnap_sse41-junction.o gsnap_sse41-concordance.o gsnap_sse41-simplepair.o gsnap_sse41-orderstat.o gsnap_sse41-intlistpool.o gsnap_sse41-uintlistpool.o gsnap_sse41-listpool.o gsnap_sse41-hitlistpool.o gsnap_sse41-pathpool.o gsnap_sse41-auxinfopool.o gsnap_sse41-pathstorepool.o gsnap_sse41-intron.o gsnap_sse41-gbuffer.o gsnap_sse41-select64-common.o gsnap_sse41-select64-ones.o gsnap_sse41-select64-zeroes.o gsnap_sse41-ef64.o gsnap_sse41-nr-x.o gsnap_sse41-knownsplicing.o gsnap_sse41-knownindels.o gsnap_sse41-splice.o gsnap_sse41-indel.o gsnap_sse41-spliceendsgen.o gsnap_sse41-spliceends.o gsnap_sse41-bitpack64-access.o gsnap_sse41-trdiag.o gsnap_sse41-trdiagpool.o gsnap_sse41-tr-extension-search.o gsnap_sse41-univdiag.o gsnap_sse41-univdiagpool.o gsnap_sse41-sedgesort.o gsnap_sse41-auxinfo.o gsnap_sse41-pathstore.o gsnap_sse41-altsplice.o gsnap_sse41-path.o gsnap_sse41-pathpair.o gsnap_sse41-path-solve.o gsnap_sse41-path-fusion.o gsnap_sse41-path-trim.o gsnap_sse41-path-eval.o gsnap_sse41-pathpair-eval.o gsnap_sse41-path-print-alignment.o gsnap_sse41-path-print-m8.o gsnap_sse41-path-print-sam.o gsnap_sse41-path-learn.o gsnap_sse41-method.o gsnap_sse41-doublelist.o gsnap_sse41-bitvector.o gsnap_sse41-transcriptpool.o gsnap_sse41-exon.o gsnap_sse41-transcript.o gsnap_sse41-trpathpool.o gsnap_sse41-trpath.o gsnap_sse41-trpath-solve.o gsnap_sse41-trpath-convert.o gsnap_sse41-trpath-eval.o gsnap_sse41-transcriptome-search.o gsnap_sse41-vectorpool.o gsnap_sse41-repair.o gsnap_sse41-transcript-remap.o gsnap_sse41-transcript-velocity.o gsnap_sse41-intersect-small.o gsnap_sse41-intersect-uint2.o gsnap_sse41-intersect-approx-uint4.o gsnap_sse41-intersect-approx-indices-uint4.o gsnap_sse41-intersect-wdups-indices.o gsnap_sse41-intersect-lower-small.o gsnap_sse41-intersect-higher-small.o gsnap_sse41-intersect-indices-small.o gsnap_sse41-intersect-indices2-small.o gsnap_sse41-intersect-concordance-uint4.o gsnap_sse41-kmer-search.o gsnap_sse41-extension-search.o gsnap_sse41-repetitive.o gsnap_sse41-uint8table.o gsnap_sse41-uinttable.o gsnap_sse41-stage1hr.o gsnap_sse41-stage1hr-single.o gsnap_sse41-stage1hr-paired.o gsnap_sse41-uinttableuint.o gsnap_sse41-tableuint.o gsnap_sse41-single-cell.o gsnap_sse41-request.o gsnap_sse41-resulthr.o gsnap_sse41-output.o gsnap_sse41-inbuffer.o gsnap_sse41-samheader.o gsnap_sse41-printbuffer.o gsnap_sse41-outbuffer.o gsnap_sse41-uintpairtable.o gsnap_sse41-splice-count.o gsnap_sse41-support.o gsnap_sse41-datadir.o gsnap_sse41-parserange.o gsnap_sse41-getline.o gsnap_sse41-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse41 gsnapl_sse41-except.o gsnapl_sse41-assert.o gsnapl_sse41-mem.o gsnapl_sse41-intlist.o gsnapl_sse41-uintlist.o gsnapl_sse41-uint8list.o gsnapl_sse41-list.o gsnapl_sse41-littleendian.o gsnapl_sse41-bigendian.o gsnapl_sse41-univinterval.o gsnapl_sse41-interval.o gsnapl_sse41-stopwatch.o gsnapl_sse41-semaphore.o gsnapl_sse41-access.o gsnapl_sse41-filestring.o gsnapl_sse41-iit-read-univ.o gsnapl_sse41-iit-read.o gsnapl_sse41-bzip2.o gsnapl_sse41-reader.o gsnapl_sse41-genomicpos.o gsnapl_sse41-compress.o gsnapl_sse41-genome.o gsnapl_sse41-transcriptome.o gsnapl_sse41-popcount.o gsnapl_sse41-genomebits.o gsnapl_sse41-genomebits_consec.o gsnapl_sse41-genomebits_count.o gsnapl_sse41-genomebits_kmer.o gsnapl_sse41-genomebits_indel.o gsnapl_sse41-genomebits_decode.o gsnapl_sse41-genomebits_mismatches.o gsnapl_sse41-genomebits_trim.o gsnapl_sse41-dinucl_bits.o gsnapl_sse41-genome_sites.o gsnapl_sse41-bitpack64-read.o gsnapl_sse41-bitpack64-readtwo.o gsnapl_sse41-mergeinfo.o gsnapl_sse41-merge-diagonals-heap-uint8.o gsnapl_sse41-merge-uint8.o gsnapl_sse41-merge-diagonals-simd-uint8.o gsnapl_sse41-merge-diagonals-heap-uint4.o gsnapl_sse41-merge-uint4.o gsnapl_sse41-merge-diagonals-simd-uint4.o gsnapl_sse41-indexdb.o gsnapl_sse41-localdb-read.o gsnapl_sse41-oligo.o gsnapl_sse41-chrnum.o gsnapl_sse41-maxent_hr.o gsnapl_sse41-mapq.o gsnapl_sse41-fopen.o gsnapl_sse41-shortread.o gsnapl_sse41-junction.o gsnapl_sse41-concordance.o gsnapl_sse41-simplepair.o gsnapl_sse41-orderstat.o gsnapl_sse41-intlistpool.o gsnapl_sse41-uintlistpool.o gsnapl_sse41-uint8listpool.o gsnapl_sse41-listpool.o gsnapl_sse41-hitlistpool.o gsnapl_sse41-pathpool.o gsnapl_sse41-auxinfopool.o gsnapl_sse41-pathstorepool.o gsnapl_sse41-intron.o gsnapl_sse41-gbuffer.o gsnapl_sse41-select64-common.o gsnapl_sse41-select64-ones.o gsnapl_sse41-select64-zeroes.o gsnapl_sse41-ef64.o gsnapl_sse41-nr-x.o gsnapl_sse41-knownsplicing.o gsnapl_sse41-knownindels.o gsnapl_sse41-splice.o gsnapl_sse41-indel.o gsnapl_sse41-spliceendsgen.o gsnapl_sse41-spliceends.o gsnapl_sse41-bitpack64-access.o gsnapl_sse41-trdiag.o gsnapl_sse41-trdiagpool.o gsnapl_sse41-tr-extension-search.o gsnapl_sse41-univdiag.o gsnapl_sse41-univdiagpool.o gsnapl_sse41-sedgesort.o gsnapl_sse41-auxinfo.o gsnapl_sse41-pathstore.o gsnapl_sse41-altsplice.o gsnapl_sse41-path.o gsnapl_sse41-pathpair.o gsnapl_sse41-path-solve.o gsnapl_sse41-path-fusion.o gsnapl_sse41-path-trim.o gsnapl_sse41-path-eval.o gsnapl_sse41-pathpair-eval.o gsnapl_sse41-path-print-alignment.o gsnapl_sse41-path-print-m8.o gsnapl_sse41-path-print-sam.o gsnapl_sse41-path-learn.o gsnapl_sse41-method.o gsnapl_sse41-doublelist.o gsnapl_sse41-bitvector.o gsnapl_sse41-transcriptpool.o gsnapl_sse41-exon.o gsnapl_sse41-transcript.o gsnapl_sse41-trpathpool.o gsnapl_sse41-trpath.o gsnapl_sse41-trpath-solve.o gsnapl_sse41-trpath-convert.o gsnapl_sse41-trpath-eval.o gsnapl_sse41-transcriptome-search.o gsnapl_sse41-vectorpool.o gsnapl_sse41-repair.o gsnapl_sse41-transcript-remap.o gsnapl_sse41-transcript-velocity.o gsnapl_sse41-intersect-large.o gsnapl_sse41-intersect-small.o gsnapl_sse41-intersect-uint2.o gsnapl_sse41-intersect-approx-uint4.o gsnapl_sse41-intersect-approx-uint8.o gsnapl_sse41-intersect-approx-indices-uint8.o gsnapl_sse41-intersect-wdups-indices.o gsnapl_sse41-intersect-lower-large.o gsnapl_sse41-intersect-higher-large.o gsnapl_sse41-intersect-indices-small.o gsnapl_sse41-intersect-indices2-large.o gsnapl_sse41-intersect-indices-uint8.o gsnapl_sse41-intersect-concordance-uint8.o gsnapl_sse41-kmer-search.o gsnapl_sse41-extension-search.o gsnapl_sse41-repetitive.o gsnapl_sse41-uint8table.o gsnapl_sse41-stage1hr.o gsnapl_sse41-stage1hr-single.o gsnapl_sse41-stage1hr-paired.o gsnapl_sse41-uint8tableuint.o gsnapl_sse41-tableuint.o gsnapl_sse41-single-cell.o gsnapl_sse41-request.o gsnapl_sse41-resulthr.o gsnapl_sse41-output.o gsnapl_sse41-inbuffer.o gsnapl_sse41-samheader.o gsnapl_sse41-printbuffer.o gsnapl_sse41-outbuffer.o gsnapl_sse41-uint8pairtable.o gsnapl_sse41-splice-count.o gsnapl_sse41-support.o gsnapl_sse41-datadir.o gsnapl_sse41-parserange.o gsnapl_sse41-getline.o gsnapl_sse41-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' @@ -28251,34 +28287,34 @@ cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat -cp md_coords.pl md_coords chmod +x gmap_process chmod +x gmap_build chmod +x gmap_cat -chmod +x md_coords +cp md_coords.pl md_coords cp fa_coords.pl fa_coords -cp psl_splicesites.pl psl_splicesites +chmod +x md_coords chmod +x fa_coords -chmod +x psl_splicesites +cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites -cp gtf_introns.pl gtf_introns -cp gtf_genes.pl gtf_genes -cp gtf_transcript_splicesites.pl gtf_transcript_splicesites -cp gff3_splicesites.pl gff3_splicesites -cp gff3_introns.pl gff3_introns -chmod +x gtf_genes +chmod +x psl_splicesites chmod +x psl_introns chmod +x psl_genes chmod +x ensembl_genes chmod +x gtf_splicesites +cp gtf_introns.pl gtf_introns +cp gtf_genes.pl gtf_genes chmod +x gtf_introns +cp gtf_transcript_splicesites.pl gtf_transcript_splicesites +chmod +x gtf_genes chmod +x gtf_transcript_splicesites +cp gff3_splicesites.pl gff3_splicesites chmod +x gff3_splicesites -chmod +x gff3_introns +cp gff3_introns.pl gff3_introns cp gff3_genes.pl gff3_genes +chmod +x gff3_introns cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x gff3_genes @@ -28296,7 +28332,7 @@ make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' dh_auto_build --builddir build_sse42 - cd build_sse42 && make -j42 + cd build_sse42 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' @@ -28363,27 +28399,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -28434,11 +28449,32 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -28453,6 +28489,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -28473,12 +28510,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -28487,8 +28520,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -28566,10 +28597,88 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -28644,14 +28753,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -28668,8 +28769,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -../../src/iit-read.c: In function 'read_words_debug': ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -28677,19 +28776,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c @@ -28697,61 +28783,111 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -28766,7 +28902,7 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -28775,7 +28911,6 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -28788,6 +28923,19 @@ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -28805,6 +28953,15 @@ | | | long long unsigned int | %lu +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -28861,7 +29018,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -28899,6 +29055,15 @@ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c +../../src/iit-read.c: In function 'read_tree': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -28971,7 +29136,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -29008,124 +29172,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -29177,6 +29223,7 @@ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -29195,7 +29242,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -29210,25 +29256,17 @@ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ @@ -29242,6 +29280,7 @@ | | | | long long unsigned int long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -29253,15 +29292,7 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -29332,7 +29363,6 @@ 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_compute_lcp_bytes': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -29400,10 +29430,18 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -29423,7 +29461,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -29441,20 +29482,12 @@ 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -29504,6 +29537,9 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c @@ -29512,7 +29548,83 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -29602,6 +29714,9 @@ | | | long long unsigned int | %lu +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5458:70: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -29622,6 +29737,18 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -29669,6 +29796,7 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -29731,134 +29859,14 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -../../src/indexdb.c: In function 'positions_read_multiple': -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -29903,8 +29911,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -29934,12 +29940,6 @@ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -29952,13 +29952,6 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -29979,8 +29972,23 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/compress-write.c: In function 'put_compressed_one': ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ @@ -29991,11 +29999,35 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); @@ -30023,11 +30055,13 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -30047,8 +30081,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -30068,14 +30102,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -30126,16 +30158,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); @@ -30144,8 +30173,18 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -30165,14 +30204,12 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -30189,13 +30226,13 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c: In function 'copy_memory_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30221,7 +30258,6 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30248,6 +30284,12 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -30347,9 +30389,15 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -30363,22 +30411,12 @@ 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ @@ -30390,9 +30428,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -30401,8 +30436,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -30410,7 +30444,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -30427,6 +30460,7 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -30440,6 +30474,7 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -30501,6 +30536,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -30510,7 +30546,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -30561,6 +30596,112 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': @@ -30595,6 +30736,7 @@ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30661,13 +30803,14 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -30687,8 +30830,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -30708,126 +30851,9 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30846,6 +30872,7 @@ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30877,8 +30904,18 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -30979,7 +31016,6 @@ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/compress-write.c: In function 'put_compressed_one': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ @@ -30995,13 +31031,73 @@ | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -31019,6 +31115,9 @@ | | | long long unsigned int | %lu +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c:5396:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -31029,6 +31128,50 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -31158,6 +31301,7 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/bitpack64-write.c:5603:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -31184,6 +31328,12 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu ../../src/bitpack64-write.c:5645:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -31220,26 +31370,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -31247,6 +31377,10 @@ | | | | long long unsigned int long unsigned int | %lu +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -31258,108 +31392,10 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -31367,10 +31403,20 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -31390,7 +31436,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -31411,21 +31459,9 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -31482,10 +31518,237 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/compress-write.c: In function 'put_compressed_one': +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -31559,7 +31822,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -31705,239 +31967,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -31952,7 +31982,6 @@ | | | | long long unsigned int long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -31964,12 +31993,16 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -31981,6 +32014,9 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c @@ -31991,7 +32027,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -32011,6 +32046,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c @@ -32029,11 +32065,11 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -32089,6 +32125,23 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -32158,6 +32211,13 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -32188,133 +32248,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -32323,12 +32256,6 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -32547,7 +32474,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -32573,12 +32499,130 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -32590,18 +32634,29 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -32623,25 +32678,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -32699,12 +32735,6 @@ 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -32720,7 +32750,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -32751,6 +32780,7 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -32799,6 +32829,7 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -32811,9 +32842,13 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -32845,6 +32880,7 @@ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -32911,9 +32947,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -33132,9 +33165,11 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33143,6 +33178,7 @@ ../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -33158,28 +33194,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/littleendian.c: In function 'Littleendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -33200,18 +33214,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -33262,21 +33270,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33376,17 +33376,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33418,6 +33407,7 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -33492,19 +33482,65 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c @@ -33545,12 +33581,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -33558,6 +33588,12 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -33587,6 +33623,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -33607,7 +33644,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -33615,8 +33651,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -33667,9 +33701,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33746,7 +33779,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -33770,13 +33802,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33785,7 +33811,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -33883,7 +33908,10 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -33898,7 +33926,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -33907,30 +33934,39 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c @@ -33993,27 +34029,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -34033,15 +34048,35 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -34092,26 +34127,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -34211,8 +34226,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -34286,7 +34300,6 @@ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -34306,7 +34319,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -34320,6 +34332,30 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c @@ -34332,10 +34368,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c @@ -34348,6 +34380,10 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c @@ -34369,14 +34405,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c @@ -34407,6 +34435,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c @@ -34443,11 +34479,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -34455,6 +34486,31 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c @@ -34462,18 +34518,22 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); @@ -34485,14 +34545,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -34505,35 +34557,15 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -34584,10 +34616,34 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -34664,7 +34720,7 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -34688,12 +34744,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -34702,7 +34752,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -34800,20 +34849,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c @@ -34830,19 +34866,19 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c ../../src/indexdb.c: In function 'positions_read_multiple_large': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c @@ -34884,8 +34920,37 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] @@ -34915,27 +34980,6 @@ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c @@ -34944,14 +34988,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c @@ -34992,15 +35028,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -35048,16 +35075,21 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -35071,7 +35103,6 @@ | | | unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/support.c:1021:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ @@ -35084,15 +35115,36 @@ | | | unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -35111,7 +35163,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -35132,26 +35186,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c @@ -35177,6 +35213,17 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -35227,22 +35274,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -35335,8 +35366,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -35350,6 +35379,20 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -35440,7 +35483,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -35448,19 +35490,9 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c @@ -35487,7 +35519,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c +../../src/indexdb.c: In function 'positions_read_multiple': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-result.o `test -f 'result.c' || echo '../../src/'`result.c @@ -35508,7 +35544,18 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -35528,9 +35575,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -35551,14 +35595,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -35578,60 +35614,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -35731,7 +35715,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -35740,8 +35725,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -35749,7 +35732,6 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -35840,8 +35822,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -35849,6 +35830,7 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); @@ -35864,8 +35846,74 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c +../../src/indexdb.c: In function 'positions_read_multiple_large': +../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1897 | read(positions_high_fd,buffer,1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1901 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -35877,20 +35925,8 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c -../../src/indexdb.c: In function 'positions_read_multiple_large': -../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1897 | read(positions_high_fd,buffer,1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1901 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c @@ -35935,14 +35971,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -35962,8 +35990,14 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -35984,6 +36018,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -36002,6 +36038,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -36052,116 +36091,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -36170,7 +36101,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -36268,8 +36198,9 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -36284,20 +36215,125 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c @@ -36318,7 +36354,15 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c @@ -36327,14 +36371,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c @@ -36396,6 +36432,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -36403,16 +36446,29 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -36433,7 +36489,6 @@ 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -36454,6 +36509,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -36463,26 +36519,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c @@ -36502,6 +36538,111 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c @@ -36509,6 +36650,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -36559,8 +36702,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -36608,182 +36751,61 @@ | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c @@ -36794,18 +36816,25 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c -../../src/indexdb.c: In function 'positions_read_multiple_large': -../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1897 | read(positions_high_fd,buffer,1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1901 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c @@ -36814,6 +36843,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c +../../src/indexdb.c: In function 'positions_read_multiple_large': +../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1897 | read(positions_high_fd,buffer,1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1901 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c @@ -36826,13 +36862,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -36841,10 +36870,21 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -36853,10 +36893,9 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -36884,6 +36923,8 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", @@ -36905,11 +36946,6 @@ | ~~~~~~~~~~~~~ | | | int -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c @@ -36950,31 +36986,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -37022,32 +37033,37 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse42 gmap_sse42-except.o gmap_sse42-assert.o gmap_sse42-mem.o gmap_sse42-intlist.o gmap_sse42-uintlist.o gmap_sse42-list.o gmap_sse42-littleendian.o gmap_sse42-bigendian.o gmap_sse42-univinterval.o gmap_sse42-interval.o gmap_sse42-stopwatch.o gmap_sse42-semaphore.o gmap_sse42-access.o gmap_sse42-filestring.o gmap_sse42-iit-read-univ.o gmap_sse42-iit-read.o gmap_sse42-md5.o gmap_sse42-bzip2.o gmap_sse42-fopen.o gmap_sse42-sequence.o gmap_sse42-reader.o gmap_sse42-genomicpos.o gmap_sse42-compress.o gmap_sse42-compress-write.o gmap_sse42-gbuffer.o gmap_sse42-genome.o gmap_sse42-popcount.o gmap_sse42-dinucl_bits.o gmap_sse42-genome_canonical.o gmap_sse42-genome-write.o gmap_sse42-bitpack64-read.o gmap_sse42-bitpack64-readtwo.o gmap_sse42-indexdb.o gmap_sse42-oligo.o gmap_sse42-block.o gmap_sse42-chrom.o gmap_sse42-segmentpos.o gmap_sse42-chrnum.o gmap_sse42-uinttable_rh.o gmap_sse42-gregion.o gmap_sse42-match.o gmap_sse42-matchpool.o gmap_sse42-diagnostic.o gmap_sse42-stage1.o gmap_sse42-diag.o gmap_sse42-diagpool.o gmap_sse42-cmet.o gmap_sse42-atoi.o gmap_sse42-orderstat.o gmap_sse42-oligoindex_hr.o gmap_sse42-intron.o gmap_sse42-maxent.o gmap_sse42-maxent_hr.o gmap_sse42-pair.o gmap_sse42-pairpool.o gmap_sse42-cellpool.o gmap_sse42-stage2.o gmap_sse42-doublelist.o gmap_sse42-smooth.o gmap_sse42-splicestringpool.o gmap_sse42-splicetrie_build.o gmap_sse42-splicetrie.o gmap_sse42-boyer-moore.o gmap_sse42-dynprog.o gmap_sse42-dynprog_simd.o gmap_sse42-dynprog_single.o gmap_sse42-dynprog_genome.o gmap_sse42-dynprog_cdna.o gmap_sse42-dynprog_end.o gmap_sse42-translation.o gmap_sse42-pbinom.o gmap_sse42-changepoint.o gmap_sse42-stage3.o gmap_sse42-request.o gmap_sse42-result.o gmap_sse42-output.o gmap_sse42-inbuffer.o gmap_sse42-samheader.o gmap_sse42-printbuffer.o gmap_sse42-outbuffer.o gmap_sse42-chimera.o gmap_sse42-datadir.o gmap_sse42-parserange.o gmap_sse42-getline.o gmap_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse42 gmapl_sse42-except.o gmapl_sse42-assert.o gmapl_sse42-mem.o gmapl_sse42-intlist.o gmapl_sse42-uintlist.o gmapl_sse42-uint8list.o gmapl_sse42-list.o gmapl_sse42-littleendian.o gmapl_sse42-bigendian.o gmapl_sse42-univinterval.o gmapl_sse42-interval.o gmapl_sse42-stopwatch.o gmapl_sse42-semaphore.o gmapl_sse42-access.o gmapl_sse42-filestring.o gmapl_sse42-iit-read-univ.o gmapl_sse42-iit-read.o gmapl_sse42-md5.o gmapl_sse42-bzip2.o gmapl_sse42-fopen.o gmapl_sse42-sequence.o gmapl_sse42-reader.o gmapl_sse42-genomicpos.o gmapl_sse42-compress.o gmapl_sse42-compress-write.o gmapl_sse42-gbuffer.o gmapl_sse42-genome.o gmapl_sse42-popcount.o gmapl_sse42-dinucl_bits.o gmapl_sse42-genome_canonical.o gmapl_sse42-genome-write.o gmapl_sse42-bitpack64-read.o gmapl_sse42-bitpack64-readtwo.o gmapl_sse42-indexdb.o gmapl_sse42-oligo.o gmapl_sse42-block.o gmapl_sse42-chrom.o gmapl_sse42-segmentpos.o gmapl_sse42-chrnum.o gmapl_sse42-uinttable_rh.o gmapl_sse42-uint8table_rh.o gmapl_sse42-gregion.o gmapl_sse42-match.o gmapl_sse42-matchpool.o gmapl_sse42-diagnostic.o gmapl_sse42-stage1.o gmapl_sse42-diag.o gmapl_sse42-diagpool.o gmapl_sse42-cmet.o gmapl_sse42-atoi.o gmapl_sse42-orderstat.o gmapl_sse42-oligoindex_hr.o gmapl_sse42-intron.o gmapl_sse42-maxent.o gmapl_sse42-maxent_hr.o gmapl_sse42-pair.o gmapl_sse42-pairpool.o gmapl_sse42-cellpool.o gmapl_sse42-stage2.o gmapl_sse42-doublelist.o gmapl_sse42-smooth.o gmapl_sse42-splicestringpool.o gmapl_sse42-splicetrie_build.o gmapl_sse42-splicetrie.o gmapl_sse42-boyer-moore.o gmapl_sse42-dynprog.o gmapl_sse42-dynprog_simd.o gmapl_sse42-dynprog_single.o gmapl_sse42-dynprog_genome.o gmapl_sse42-dynprog_cdna.o gmapl_sse42-dynprog_end.o gmapl_sse42-translation.o gmapl_sse42-pbinom.o gmapl_sse42-changepoint.o gmapl_sse42-stage3.o gmapl_sse42-request.o gmapl_sse42-result.o gmapl_sse42-output.o gmapl_sse42-inbuffer.o gmapl_sse42-samheader.o gmapl_sse42-printbuffer.o gmapl_sse42-outbuffer.o gmapl_sse42-chimera.o gmapl_sse42-datadir.o gmapl_sse42-parserange.o gmapl_sse42-getline.o gmapl_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse42 gsnap_sse42-except.o gsnap_sse42-assert.o gsnap_sse42-mem.o gsnap_sse42-intlist.o gsnap_sse42-uintlist.o gsnap_sse42-list.o gsnap_sse42-littleendian.o gsnap_sse42-bigendian.o gsnap_sse42-univinterval.o gsnap_sse42-interval.o gsnap_sse42-stopwatch.o gsnap_sse42-semaphore.o gsnap_sse42-access.o gsnap_sse42-filestring.o gsnap_sse42-iit-read-univ.o gsnap_sse42-iit-read.o gsnap_sse42-bzip2.o gsnap_sse42-reader.o gsnap_sse42-genomicpos.o gsnap_sse42-compress.o gsnap_sse42-genome.o gsnap_sse42-transcriptome.o gsnap_sse42-popcount.o gsnap_sse42-genomebits.o gsnap_sse42-genomebits_consec.o gsnap_sse42-genomebits_count.o gsnap_sse42-genomebits_kmer.o gsnap_sse42-genomebits_indel.o gsnap_sse42-genomebits_decode.o gsnap_sse42-genomebits_mismatches.o gsnap_sse42-genomebits_trim.o gsnap_sse42-dinucl_bits.o gsnap_sse42-genome_sites.o gsnap_sse42-bitpack64-read.o gsnap_sse42-bitpack64-readtwo.o gsnap_sse42-mergeinfo.o gsnap_sse42-merge-diagonals-heap-uint4.o gsnap_sse42-merge-uint4.o gsnap_sse42-merge-diagonals-simd-uint4.o gsnap_sse42-indexdb.o gsnap_sse42-localdb-read.o gsnap_sse42-oligo.o gsnap_sse42-chrnum.o gsnap_sse42-maxent_hr.o gsnap_sse42-mapq.o gsnap_sse42-fopen.o gsnap_sse42-shortread.o gsnap_sse42-junction.o gsnap_sse42-concordance.o gsnap_sse42-simplepair.o gsnap_sse42-orderstat.o gsnap_sse42-intlistpool.o gsnap_sse42-uintlistpool.o gsnap_sse42-listpool.o gsnap_sse42-hitlistpool.o gsnap_sse42-pathpool.o gsnap_sse42-auxinfopool.o gsnap_sse42-pathstorepool.o gsnap_sse42-intron.o gsnap_sse42-gbuffer.o gsnap_sse42-select64-common.o gsnap_sse42-select64-ones.o gsnap_sse42-select64-zeroes.o gsnap_sse42-ef64.o gsnap_sse42-nr-x.o gsnap_sse42-knownsplicing.o gsnap_sse42-knownindels.o gsnap_sse42-splice.o gsnap_sse42-indel.o gsnap_sse42-spliceendsgen.o gsnap_sse42-spliceends.o gsnap_sse42-bitpack64-access.o gsnap_sse42-trdiag.o gsnap_sse42-trdiagpool.o gsnap_sse42-tr-extension-search.o gsnap_sse42-univdiag.o gsnap_sse42-univdiagpool.o gsnap_sse42-sedgesort.o gsnap_sse42-auxinfo.o gsnap_sse42-pathstore.o gsnap_sse42-altsplice.o gsnap_sse42-path.o gsnap_sse42-pathpair.o gsnap_sse42-path-solve.o gsnap_sse42-path-fusion.o gsnap_sse42-path-trim.o gsnap_sse42-path-eval.o gsnap_sse42-pathpair-eval.o gsnap_sse42-path-print-alignment.o gsnap_sse42-path-print-m8.o gsnap_sse42-path-print-sam.o gsnap_sse42-path-learn.o gsnap_sse42-method.o gsnap_sse42-doublelist.o gsnap_sse42-bitvector.o gsnap_sse42-transcriptpool.o gsnap_sse42-exon.o gsnap_sse42-transcript.o gsnap_sse42-trpathpool.o gsnap_sse42-trpath.o gsnap_sse42-trpath-solve.o gsnap_sse42-trpath-convert.o gsnap_sse42-trpath-eval.o gsnap_sse42-transcriptome-search.o gsnap_sse42-vectorpool.o gsnap_sse42-repair.o gsnap_sse42-transcript-remap.o gsnap_sse42-transcript-velocity.o gsnap_sse42-intersect-small.o gsnap_sse42-intersect-uint2.o gsnap_sse42-intersect-approx-uint4.o gsnap_sse42-intersect-approx-indices-uint4.o gsnap_sse42-intersect-wdups-indices.o gsnap_sse42-intersect-lower-small.o gsnap_sse42-intersect-higher-small.o gsnap_sse42-intersect-indices-small.o gsnap_sse42-intersect-indices2-small.o gsnap_sse42-intersect-concordance-uint4.o gsnap_sse42-kmer-search.o gsnap_sse42-extension-search.o gsnap_sse42-repetitive.o gsnap_sse42-uint8table.o gsnap_sse42-uinttable.o gsnap_sse42-stage1hr.o gsnap_sse42-stage1hr-single.o gsnap_sse42-stage1hr-paired.o gsnap_sse42-uinttableuint.o gsnap_sse42-tableuint.o gsnap_sse42-single-cell.o gsnap_sse42-request.o gsnap_sse42-resulthr.o gsnap_sse42-output.o gsnap_sse42-inbuffer.o gsnap_sse42-samheader.o gsnap_sse42-printbuffer.o gsnap_sse42-outbuffer.o gsnap_sse42-uintpairtable.o gsnap_sse42-splice-count.o gsnap_sse42-support.o gsnap_sse42-datadir.o gsnap_sse42-parserange.o gsnap_sse42-getline.o gsnap_sse42-gsnap.o -lz -lbz2 -lm -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -37073,6 +37089,26 @@ | | | unsigned int | %lu +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse42 gsnapl_sse42-except.o gsnapl_sse42-assert.o gsnapl_sse42-mem.o gsnapl_sse42-intlist.o gsnapl_sse42-uintlist.o gsnapl_sse42-uint8list.o gsnapl_sse42-list.o gsnapl_sse42-littleendian.o gsnapl_sse42-bigendian.o gsnapl_sse42-univinterval.o gsnapl_sse42-interval.o gsnapl_sse42-stopwatch.o gsnapl_sse42-semaphore.o gsnapl_sse42-access.o gsnapl_sse42-filestring.o gsnapl_sse42-iit-read-univ.o gsnapl_sse42-iit-read.o gsnapl_sse42-bzip2.o gsnapl_sse42-reader.o gsnapl_sse42-genomicpos.o gsnapl_sse42-compress.o gsnapl_sse42-genome.o gsnapl_sse42-transcriptome.o gsnapl_sse42-popcount.o gsnapl_sse42-genomebits.o gsnapl_sse42-genomebits_consec.o gsnapl_sse42-genomebits_count.o gsnapl_sse42-genomebits_kmer.o gsnapl_sse42-genomebits_indel.o gsnapl_sse42-genomebits_decode.o gsnapl_sse42-genomebits_mismatches.o gsnapl_sse42-genomebits_trim.o gsnapl_sse42-dinucl_bits.o gsnapl_sse42-genome_sites.o gsnapl_sse42-bitpack64-read.o gsnapl_sse42-bitpack64-readtwo.o gsnapl_sse42-mergeinfo.o gsnapl_sse42-merge-diagonals-heap-uint8.o gsnapl_sse42-merge-uint8.o gsnapl_sse42-merge-diagonals-simd-uint8.o gsnapl_sse42-merge-diagonals-heap-uint4.o gsnapl_sse42-merge-uint4.o gsnapl_sse42-merge-diagonals-simd-uint4.o gsnapl_sse42-indexdb.o gsnapl_sse42-localdb-read.o gsnapl_sse42-oligo.o gsnapl_sse42-chrnum.o gsnapl_sse42-maxent_hr.o gsnapl_sse42-mapq.o gsnapl_sse42-fopen.o gsnapl_sse42-shortread.o gsnapl_sse42-junction.o gsnapl_sse42-concordance.o gsnapl_sse42-simplepair.o gsnapl_sse42-orderstat.o gsnapl_sse42-intlistpool.o gsnapl_sse42-uintlistpool.o gsnapl_sse42-uint8listpool.o gsnapl_sse42-listpool.o gsnapl_sse42-hitlistpool.o gsnapl_sse42-pathpool.o gsnapl_sse42-auxinfopool.o gsnapl_sse42-pathstorepool.o gsnapl_sse42-intron.o gsnapl_sse42-gbuffer.o gsnapl_sse42-select64-common.o gsnapl_sse42-select64-ones.o gsnapl_sse42-select64-zeroes.o gsnapl_sse42-ef64.o gsnapl_sse42-nr-x.o gsnapl_sse42-knownsplicing.o gsnapl_sse42-knownindels.o gsnapl_sse42-splice.o gsnapl_sse42-indel.o gsnapl_sse42-spliceendsgen.o gsnapl_sse42-spliceends.o gsnapl_sse42-bitpack64-access.o gsnapl_sse42-trdiag.o gsnapl_sse42-trdiagpool.o gsnapl_sse42-tr-extension-search.o gsnapl_sse42-univdiag.o gsnapl_sse42-univdiagpool.o gsnapl_sse42-sedgesort.o gsnapl_sse42-auxinfo.o gsnapl_sse42-pathstore.o gsnapl_sse42-altsplice.o gsnapl_sse42-path.o gsnapl_sse42-pathpair.o gsnapl_sse42-path-solve.o gsnapl_sse42-path-fusion.o gsnapl_sse42-path-trim.o gsnapl_sse42-path-eval.o gsnapl_sse42-pathpair-eval.o gsnapl_sse42-path-print-alignment.o gsnapl_sse42-path-print-m8.o gsnapl_sse42-path-print-sam.o gsnapl_sse42-path-learn.o gsnapl_sse42-method.o gsnapl_sse42-doublelist.o gsnapl_sse42-bitvector.o gsnapl_sse42-transcriptpool.o gsnapl_sse42-exon.o gsnapl_sse42-transcript.o gsnapl_sse42-trpathpool.o gsnapl_sse42-trpath.o gsnapl_sse42-trpath-solve.o gsnapl_sse42-trpath-convert.o gsnapl_sse42-trpath-eval.o gsnapl_sse42-transcriptome-search.o gsnapl_sse42-vectorpool.o gsnapl_sse42-repair.o gsnapl_sse42-transcript-remap.o gsnapl_sse42-transcript-velocity.o gsnapl_sse42-intersect-large.o gsnapl_sse42-intersect-small.o gsnapl_sse42-intersect-uint2.o gsnapl_sse42-intersect-approx-uint4.o gsnapl_sse42-intersect-approx-uint8.o gsnapl_sse42-intersect-approx-indices-uint8.o gsnapl_sse42-intersect-wdups-indices.o gsnapl_sse42-intersect-lower-large.o gsnapl_sse42-intersect-higher-large.o gsnapl_sse42-intersect-indices-small.o gsnapl_sse42-intersect-indices2-large.o gsnapl_sse42-intersect-indices-uint8.o gsnapl_sse42-intersect-concordance-uint8.o gsnapl_sse42-kmer-search.o gsnapl_sse42-extension-search.o gsnapl_sse42-repetitive.o gsnapl_sse42-uint8table.o gsnapl_sse42-stage1hr.o gsnapl_sse42-stage1hr-single.o gsnapl_sse42-stage1hr-paired.o gsnapl_sse42-uint8tableuint.o gsnapl_sse42-tableuint.o gsnapl_sse42-single-cell.o gsnapl_sse42-request.o gsnapl_sse42-resulthr.o gsnapl_sse42-output.o gsnapl_sse42-inbuffer.o gsnapl_sse42-samheader.o gsnapl_sse42-printbuffer.o gsnapl_sse42-outbuffer.o gsnapl_sse42-uint8pairtable.o gsnapl_sse42-splice-count.o gsnapl_sse42-support.o gsnapl_sse42-datadir.o gsnapl_sse42-parserange.o gsnapl_sse42-getline.o gsnapl_sse42-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' @@ -37080,42 +37116,42 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build +chmod +x gmap_process +chmod +x gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords -cp psl_splicesites.pl psl_splicesites -chmod +x gmap_process -cp psl_introns.pl psl_introns -cp psl_genes.pl psl_genes -chmod +x gmap_build chmod +x gmap_cat chmod +x md_coords chmod +x fa_coords -chmod +x psl_splicesites +cp psl_splicesites.pl psl_splicesites +cp psl_introns.pl psl_introns +cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes +chmod +x psl_splicesites chmod +x psl_introns chmod +x psl_genes +chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns -cp gtf_genes.pl gtf_genes -cp gtf_transcript_splicesites.pl gtf_transcript_splicesites -chmod +x ensembl_genes -cp gff3_splicesites.pl gff3_splicesites -cp gff3_introns.pl gff3_introns chmod +x gtf_splicesites -cp gff3_genes.pl gff3_genes chmod +x gtf_introns +cp gtf_genes.pl gtf_genes +cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes +cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites -cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_splicesites +cp gff3_introns.pl gff3_introns +cp gff3_genes.pl gff3_genes chmod +x gff3_introns chmod +x gff3_genes +cp dbsnp_iit.pl dbsnp_iit +chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit -chmod +x dbsnp_iit -chmod +x vcf_iit chmod +x gvf_iit +chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/util' Making all in tests make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/tests' @@ -37126,7 +37162,7 @@ make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' dh_auto_build --builddir build_avx2 - cd build_avx2 && make -j42 + cd build_avx2 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' @@ -37166,17 +37202,24 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ @@ -37187,8 +37230,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -37196,7 +37240,6 @@ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -37209,15 +37252,49 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_memory_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -37267,53 +37344,166 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +../../src/access.c: In function 'copy_memory_from_file': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -37322,6 +37512,8 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -37329,7 +37521,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -37408,6 +37600,7 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -37420,7 +37613,9 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -37513,7 +37708,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -37521,184 +37715,141 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/compress-write.c: In function 'put_compressed_one': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c -../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -37725,12 +37876,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5396:86: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -37741,6 +37886,13 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -37777,6 +37929,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -37922,6 +38075,22 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -37933,24 +38102,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -37958,6 +38109,7 @@ | | | | long long unsigned int long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -37969,133 +38121,10 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -38233,10 +38262,15 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -38256,11 +38290,9 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -38280,8 +38312,9 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -38317,7 +38350,6 @@ ../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -38333,14 +38365,14 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -38440,12 +38472,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -38483,8 +38511,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5424:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -38521,12 +38547,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c:5458:41: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -38563,13 +38583,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -38653,6 +38666,50 @@ | ~ | | | Oligospace_T {aka long unsigned int} +../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] + 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu +../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] + 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5646 | n,n/BLOCKSIZE,totalcount,nextpage); + | ~~~~~~~~~~ + | | + | UINT8 {aka long unsigned int} +../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] + 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", + | ~~~^ + | | + | long long unsigned int + | %lu + 5646 | n,n/BLOCKSIZE,totalcount,nextpage); + | ~~~~~~~~ + | | + | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -38683,38 +38740,12 @@ 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': -../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] - 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ -../../src/bitpack64-write.c:5645:71: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] - 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5646 | n,n/BLOCKSIZE,totalcount,nextpage); - | ~~~~~~~~~~ - | | - | UINT8 {aka long unsigned int} -../../src/bitpack64-write.c:5645:88: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] - 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", - | ~~~^ - | | - | long long unsigned int - | %lu - 5646 | n,n/BLOCKSIZE,totalcount,nextpage); - | ~~~~~~~~ - | | - | UINT8 {aka long unsigned int} ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -38749,21 +38780,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu ../../src/iit-read.c: In function 'IIT_debug': -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -38783,17 +38800,8 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -38808,6 +38816,10 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -38816,8 +38828,32 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c @@ -38825,8 +38861,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); @@ -38854,7 +38888,10 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -38874,11 +38911,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -38899,14 +38932,14 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -38923,7 +38956,6 @@ ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -38958,18 +38990,29 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c +../../src/iit_store.c: In function 'parse_fasta': +../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 689 | fprintf(stderr,"Assigning %llu to end\n",end); + | ~~~^ ~~~ + | | | + | | Univcoord_T {aka long unsigned int} + | long long unsigned int + | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_char': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -38988,16 +39031,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/iit_store.c: In function 'parse_fasta': -../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 689 | fprintf(stderr,"Assigning %llu to end\n",end); - | ~~~^ ~~~ - | | | - | | Univcoord_T {aka long unsigned int} - | long long unsigned int - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -39018,6 +39051,9 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -39025,9 +39061,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -39053,6 +39086,7 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -39078,10 +39112,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -39133,7 +39167,6 @@ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -39182,26 +39215,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -39221,9 +39234,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -39232,7 +39243,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -39240,6 +39250,8 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -39256,6 +39268,8 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -39269,7 +39283,6 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -39283,6 +39296,10 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -39290,6 +39307,10 @@ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -39302,16 +39323,27 @@ ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -39319,7 +39351,7 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -39333,6 +39365,10 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c @@ -39392,10 +39428,106 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -39404,7 +39536,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -39412,6 +39543,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -39425,10 +39557,10 @@ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -39442,6 +39574,7 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -39483,6 +39616,7 @@ ../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -39490,7 +39624,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -39504,130 +39637,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -39648,6 +39658,32 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c @@ -39655,7 +39691,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -39706,10 +39741,132 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -39785,6 +39942,12 @@ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_annotations': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -39809,34 +39972,9 @@ | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -39920,7 +40058,6 @@ | ~ | | | Oligospace_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/bitpack64-write.c:5458:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -39947,6 +40084,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -40056,11 +40194,14 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] @@ -40070,12 +40211,14 @@ | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -40087,121 +40230,8 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -40213,6 +40243,9 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -40232,11 +40265,12 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -40253,6 +40287,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -40288,7 +40324,6 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -40313,11 +40348,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -40410,7 +40440,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c: In function 'put_compressed_one': ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -40418,6 +40447,9 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ @@ -40431,123 +40463,19 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -40740,6 +40668,8 @@ | ~ | | | Oligospace_T {aka long unsigned int} +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bitpack64-write.c:5645:53: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -40766,6 +40696,113 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -40773,7 +40810,6 @@ | | | | long long unsigned int long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -40781,10 +40817,7 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -40796,10 +40829,18 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -40811,31 +40852,15 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -40848,10 +40873,16 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -40866,15 +40897,14 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -40925,15 +40955,26 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/compress-write.c: In function 'put_compressed_one': +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); @@ -40941,23 +40982,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -41007,6 +41031,15 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -41055,7 +41088,108 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -41274,107 +41408,8 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -41400,6 +41435,7 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -41408,6 +41444,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -41419,8 +41457,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c @@ -41434,7 +41470,26 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -41454,29 +41509,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c @@ -41537,92 +41573,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -41732,13 +41682,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge_bitpacks': ../../src/bitpack64-write.c:5574:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -41776,19 +41719,6 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/bitpack64-write.c:5603:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ @@ -41861,9 +41791,91 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -41927,12 +41939,20 @@ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -41963,8 +41983,23 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -41979,6 +42014,7 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c @@ -41986,8 +42022,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -42007,22 +42041,18 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/bigendian.c: In function 'Bigendian_write_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ @@ -42038,9 +42068,13 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/access.c: In function 'copy_memory_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -42090,9 +42124,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -42169,6 +42202,7 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -42192,8 +42226,20 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -42210,6 +42256,9 @@ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -42219,12 +42268,20 @@ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -42286,6 +42343,7 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -42299,21 +42357,14 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c @@ -42322,21 +42373,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c @@ -42374,11 +42410,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -42386,6 +42417,11 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -42418,6 +42454,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -42438,12 +42476,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -42494,6 +42528,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c @@ -42501,6 +42537,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -42509,6 +42546,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -42516,8 +42554,63 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -42548,6 +42641,15 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -42592,93 +42694,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -42693,7 +42708,6 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -42706,20 +42720,33 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -42742,15 +42769,21 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -42758,6 +42791,9 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c @@ -42801,13 +42837,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -42815,6 +42844,13 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -42822,11 +42858,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -42846,7 +42877,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -42866,12 +42901,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -42922,100 +42956,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -43108,13 +43048,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -43122,6 +43055,100 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -43135,7 +43162,12 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -43150,6 +43182,10 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c @@ -43166,12 +43202,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c @@ -43218,6 +43254,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -43226,7 +43263,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c @@ -43270,8 +43306,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -43279,14 +43313,13 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -43307,12 +43340,14 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -43332,10 +43367,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -../../src/bigendian.c: In function 'Bigendian_write_char': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -43352,15 +43388,13 @@ 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -43386,7 +43420,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -43412,11 +43445,113 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c @@ -43436,6 +43571,7 @@ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -43493,6 +43629,7 @@ ../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -43528,7 +43665,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -43542,108 +43678,8 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c @@ -43694,8 +43730,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -43704,6 +43738,8 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c @@ -43714,6 +43750,33 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -43741,45 +43804,10 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c @@ -43789,6 +43817,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c @@ -43818,9 +43854,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -43868,12 +43901,14 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -43881,31 +43916,11 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -43931,17 +43946,37 @@ | | | unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -43961,11 +43996,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -43982,6 +44017,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c @@ -43998,6 +44034,56 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c @@ -44009,23 +44095,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44131,42 +44200,17 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44199,7 +44243,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -44260,30 +44303,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -44291,6 +44310,23 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c @@ -44300,12 +44336,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c @@ -44359,7 +44395,6 @@ 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -44380,6 +44415,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -44387,11 +44428,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c @@ -44467,7 +44503,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44567,48 +44602,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44714,10 +44708,49 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -44725,6 +44758,9 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c @@ -44760,19 +44796,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -44792,10 +44820,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -44816,6 +44842,9 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -44825,14 +44854,76 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -44932,7 +45023,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -45038,60 +45128,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/access.c: In function 'copy_memory_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c @@ -45126,15 +45162,15 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c @@ -45162,6 +45198,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -45170,8 +45208,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c @@ -45232,7 +45268,27 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c @@ -45256,26 +45312,6 @@ 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -45298,6 +45334,7 @@ | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -45305,7 +45342,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c @@ -45328,71 +45364,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -45492,23 +45463,13 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -45517,7 +45478,6 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -45525,22 +45485,47 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read.c: In function 'read_tree': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -45554,7 +45539,32 @@ ../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -45615,9 +45625,42 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c +../../src/indexdb.c: In function 'positions_read_multiple_large': +../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1897 | read(positions_high_fd,buffer,1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1901 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c @@ -45633,13 +45676,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c -../../src/indexdb.c: In function 'positions_read_multiple_large': -../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1897 | read(positions_high_fd,buffer,1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1901 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c @@ -45659,6 +45695,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -45667,14 +45709,9 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -45683,18 +45720,40 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c +../../src/altsplice.c: In function 'Altsplice_print': +../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~^ + | | + | int + | %ld + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~~~~~~~~~~ + | | + | Univcoord_T {aka long unsigned int} +../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] + 124 | printf(":%u,len:%d,%llu(%d,%d)", + | ~~~^ + | | + | long long unsigned int + | %u + 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); + | ~~~~~~~~~~~~~ + | | + | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -45722,33 +45781,10 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c -../../src/altsplice.c: In function 'Altsplice_print': -../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~^ - | | - | int - | %ld - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~~~~~~~~~~ - | | - | Univcoord_T {aka long unsigned int} -../../src/altsplice.c:124:29: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'int' [-Wformat=] - 124 | printf(":%u,len:%d,%llu(%d,%d)", - | ~~~^ - | | - | long long unsigned int - | %u - 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); - | ~~~~~~~~~~~~~ - | | - | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c @@ -45781,6 +45817,12 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -45828,18 +45870,30 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm -gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-dinucl_bits.o gmap_avx2-genome_canonical.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-printbuffer.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-dinucl_bits.o gmapl_avx2-genome_canonical.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-uint8table_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-printbuffer.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genomebits.o gsnap_avx2-genomebits_consec.o gsnap_avx2-genomebits_count.o gsnap_avx2-genomebits_kmer.o gsnap_avx2-genomebits_indel.o gsnap_avx2-genomebits_decode.o gsnap_avx2-genomebits_mismatches.o gsnap_avx2-genomebits_trim.o gsnap_avx2-dinucl_bits.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-mergeinfo.o gsnap_avx2-merge-diagonals-heap-uint4.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-localdb-read.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-junction.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-pathpool.o gsnap_avx2-auxinfopool.o gsnap_avx2-pathstorepool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-select64-common.o gsnap_avx2-select64-ones.o gsnap_avx2-select64-zeroes.o gsnap_avx2-ef64.o gsnap_avx2-nr-x.o gsnap_avx2-knownsplicing.o gsnap_avx2-knownindels.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-spliceendsgen.o gsnap_avx2-spliceends.o gsnap_avx2-bitpack64-access.o gsnap_avx2-trdiag.o gsnap_avx2-trdiagpool.o gsnap_avx2-tr-extension-search.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-auxinfo.o gsnap_avx2-pathstore.o gsnap_avx2-altsplice.o gsnap_avx2-path.o gsnap_avx2-pathpair.o gsnap_avx2-path-solve.o gsnap_avx2-path-fusion.o gsnap_avx2-path-trim.o gsnap_avx2-path-eval.o gsnap_avx2-pathpair-eval.o gsnap_avx2-path-print-alignment.o gsnap_avx2-path-print-m8.o gsnap_avx2-path-print-sam.o gsnap_avx2-path-learn.o gsnap_avx2-method.o gsnap_avx2-doublelist.o gsnap_avx2-bitvector.o gsnap_avx2-transcriptpool.o gsnap_avx2-exon.o gsnap_avx2-transcript.o gsnap_avx2-trpathpool.o gsnap_avx2-trpath.o gsnap_avx2-trpath-solve.o gsnap_avx2-trpath-convert.o gsnap_avx2-trpath-eval.o gsnap_avx2-transcriptome-search.o gsnap_avx2-vectorpool.o gsnap_avx2-repair.o gsnap_avx2-transcript-remap.o gsnap_avx2-transcript-velocity.o gsnap_avx2-intersect-small.o gsnap_avx2-intersect-uint2.o gsnap_avx2-intersect-approx-uint4.o gsnap_avx2-intersect-approx-indices-uint4.o gsnap_avx2-intersect-wdups-indices.o gsnap_avx2-intersect-lower-small.o gsnap_avx2-intersect-higher-small.o gsnap_avx2-intersect-indices-small.o gsnap_avx2-intersect-indices2-small.o gsnap_avx2-intersect-concordance-uint4.o gsnap_avx2-kmer-search.o gsnap_avx2-extension-search.o gsnap_avx2-repetitive.o gsnap_avx2-uint8table.o gsnap_avx2-uinttable.o gsnap_avx2-stage1hr.o gsnap_avx2-stage1hr-single.o gsnap_avx2-stage1hr-paired.o gsnap_avx2-uinttableuint.o gsnap_avx2-tableuint.o gsnap_avx2-single-cell.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-printbuffer.o gsnap_avx2-outbuffer.o gsnap_avx2-uintpairtable.o gsnap_avx2-splice-count.o gsnap_avx2-support.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-gsnap.o -lz -lbz2 -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -45860,24 +45914,6 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-dinucl_bits.o gmap_avx2-genome_canonical.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-printbuffer.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-dinucl_bits.o gmapl_avx2-genome_canonical.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-uint8table_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-printbuffer.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genomebits.o gsnap_avx2-genomebits_consec.o gsnap_avx2-genomebits_count.o gsnap_avx2-genomebits_kmer.o gsnap_avx2-genomebits_indel.o gsnap_avx2-genomebits_decode.o gsnap_avx2-genomebits_mismatches.o gsnap_avx2-genomebits_trim.o gsnap_avx2-dinucl_bits.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-mergeinfo.o gsnap_avx2-merge-diagonals-heap-uint4.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-localdb-read.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-junction.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-pathpool.o gsnap_avx2-auxinfopool.o gsnap_avx2-pathstorepool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-select64-common.o gsnap_avx2-select64-ones.o gsnap_avx2-select64-zeroes.o gsnap_avx2-ef64.o gsnap_avx2-nr-x.o gsnap_avx2-knownsplicing.o gsnap_avx2-knownindels.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-spliceendsgen.o gsnap_avx2-spliceends.o gsnap_avx2-bitpack64-access.o gsnap_avx2-trdiag.o gsnap_avx2-trdiagpool.o gsnap_avx2-tr-extension-search.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-auxinfo.o gsnap_avx2-pathstore.o gsnap_avx2-altsplice.o gsnap_avx2-path.o gsnap_avx2-pathpair.o gsnap_avx2-path-solve.o gsnap_avx2-path-fusion.o gsnap_avx2-path-trim.o gsnap_avx2-path-eval.o gsnap_avx2-pathpair-eval.o gsnap_avx2-path-print-alignment.o gsnap_avx2-path-print-m8.o gsnap_avx2-path-print-sam.o gsnap_avx2-path-learn.o gsnap_avx2-method.o gsnap_avx2-doublelist.o gsnap_avx2-bitvector.o gsnap_avx2-transcriptpool.o gsnap_avx2-exon.o gsnap_avx2-transcript.o gsnap_avx2-trpathpool.o gsnap_avx2-trpath.o gsnap_avx2-trpath-solve.o gsnap_avx2-trpath-convert.o gsnap_avx2-trpath-eval.o gsnap_avx2-transcriptome-search.o gsnap_avx2-vectorpool.o gsnap_avx2-repair.o gsnap_avx2-transcript-remap.o gsnap_avx2-transcript-velocity.o gsnap_avx2-intersect-small.o gsnap_avx2-intersect-uint2.o gsnap_avx2-intersect-approx-uint4.o gsnap_avx2-intersect-approx-indices-uint4.o gsnap_avx2-intersect-wdups-indices.o gsnap_avx2-intersect-lower-small.o gsnap_avx2-intersect-higher-small.o gsnap_avx2-intersect-indices-small.o gsnap_avx2-intersect-indices2-small.o gsnap_avx2-intersect-concordance-uint4.o gsnap_avx2-kmer-search.o gsnap_avx2-extension-search.o gsnap_avx2-repetitive.o gsnap_avx2-uint8table.o gsnap_avx2-uinttable.o gsnap_avx2-stage1hr.o gsnap_avx2-stage1hr-single.o gsnap_avx2-stage1hr-paired.o gsnap_avx2-uinttableuint.o gsnap_avx2-tableuint.o gsnap_avx2-single-cell.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-printbuffer.o gsnap_avx2-outbuffer.o gsnap_avx2-uintpairtable.o gsnap_avx2-splice-count.o gsnap_avx2-support.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-gsnap.o -lz -lbz2 -lm -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -45911,39 +45947,39 @@ cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build cp gmap_cat.pl gmap_cat -cp md_coords.pl md_coords -chmod +x gmap_process chmod +x gmap_build +chmod +x gmap_process chmod +x gmap_cat -chmod +x md_coords +cp md_coords.pl md_coords cp fa_coords.pl fa_coords +chmod +x md_coords +chmod +x fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes -chmod +x fa_coords -cp ensembl_genes.pl ensembl_genes -chmod +x psl_splicesites chmod +x psl_introns +chmod +x psl_splicesites chmod +x psl_genes -chmod +x ensembl_genes +cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites +chmod +x ensembl_genes cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites cp gtf_genes.pl gtf_genes -cp gtf_transcript_splicesites.pl gtf_transcript_splicesites -chmod +x gtf_genes -cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_introns +chmod +x gtf_genes +cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_transcript_splicesites +cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites chmod +x gff3_introns cp gff3_genes.pl gff3_genes -chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit +chmod +x gff3_genes +chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit -chmod +x dbsnp_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/util' @@ -45956,7 +45992,7 @@ make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' dh_auto_build --builddir build_avx512 - cd build_avx512 && make -j42 + cd build_avx512 && make -j40 make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' @@ -45998,14 +46034,100 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c ../../src/access.c: In function 'copy_memory_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46055,69 +46177,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -46217,40 +46276,12 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -46301,14 +46332,9 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -46317,6 +46343,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -46324,6 +46351,7 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -46360,6 +46388,7 @@ ../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46373,6 +46402,7 @@ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46402,6 +46432,7 @@ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46414,17 +46445,19 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46492,6 +46525,7 @@ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +../../src/compress-write.c: In function 'Compress_compress': ../../src/iit-read-univ.c: In function 'read_words': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -46515,34 +46549,20 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c ../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': ../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -46590,6 +46610,8 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': ../../src/bitpack64-write.c:5424:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -46663,6 +46685,12 @@ | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ ../../src/bitpack64-write.c:5574:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -46761,16 +46789,58 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46778,14 +46848,16 @@ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -46876,50 +46948,14 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -47026,6 +47062,7 @@ ../../src/sarray-write.c:1336:5: note: in expansion of macro 'FREAD_UINTS' 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -47039,6 +47076,7 @@ 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function 'Sarray_discriminating_chars': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -47057,15 +47095,52 @@ ../../src/sarray-write.c:2443:5: note: in expansion of macro 'FREAD_UINT' 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c @@ -47073,11 +47148,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -47128,45 +47200,120 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -47259,7 +47406,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -47267,9 +47413,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -47488,64 +47633,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -47553,33 +47641,6 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -47587,48 +47648,6 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -47643,7 +47662,18 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} +../../src/indexdb.c: In function 'positions_read_multiple': In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -47652,8 +47682,15 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/indexdb-cat.c: In function 'main': ../../src/indexdb-cat.c:823:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); @@ -47681,7 +47718,6 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c @@ -47698,7 +47734,6 @@ ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); @@ -47706,8 +47741,11 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -47716,7 +47754,6 @@ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -47729,11 +47766,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -47784,7 +47821,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c @@ -47797,11 +47833,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/iit_store.c: In function 'parse_fasta': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit_store.c:689:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ @@ -47828,8 +47861,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -47850,14 +47882,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -47884,6 +47914,7 @@ 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -47908,10 +47939,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -48004,6 +48036,7 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -48011,10 +48044,17 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); @@ -48030,11 +48070,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -48043,7 +48078,6 @@ ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); @@ -48054,6 +48088,7 @@ | ^~~~~~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48067,6 +48102,8 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -48119,7 +48156,6 @@ ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48145,7 +48181,6 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -48159,6 +48194,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -48167,8 +48203,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -48219,14 +48253,9 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -48319,7 +48348,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -48327,9 +48355,20 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -48349,20 +48388,10 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -48375,10 +48404,18 @@ ../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -48386,8 +48423,8 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/iit-read.c: In function 'read_tree': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48400,7 +48437,6 @@ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48437,6 +48473,7 @@ ../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -48472,16 +48509,17 @@ ../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -48532,6 +48570,33 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -48631,142 +48696,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -48985,6 +48914,124 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -48999,10 +49046,6 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -49014,35 +49057,15 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -49062,7 +49085,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -49083,6 +49106,19 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -49090,6 +49126,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -49140,9 +49178,11 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -49256,6 +49296,7 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -49264,143 +49305,11 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/indexdb-write.c: In function 'Indexdb_write_offsets': -../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': -../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] - 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); - | ~~~^ ~~~~~~~~~~~~~~ - | | | - | long long unsigned int long unsigned int - | %lu -../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': -../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] - 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", - | ~~~^ - | | - | long long unsigned int - | %lu - 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); - | ~~~~~~~~~~~ - | | - | Hugepositionsptr_T {aka long unsigned int} ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -49619,140 +49528,7 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -../../src/access.c: In function 'copy_memory_from_file': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -49761,6 +49537,14 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +../../src/indexdb-write.c: In function 'Indexdb_write_offsets': +../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -49768,6 +49552,13 @@ ../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': +../../src/indexdb-write.c:1179:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] + 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); + | ~~~^ ~~~~~~~~~~~~~~ + | | | + | long long unsigned int long unsigned int + | %lu ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -49785,6 +49576,7 @@ 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': +../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -49811,6 +49603,16 @@ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': +../../src/indexdb-write.c:2867:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] + 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", + | ~~~^ + | | + | long long unsigned int + | %lu + 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); + | ~~~~~~~~~~~ + | | + | Hugepositionsptr_T {aka long unsigned int} ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -49858,6 +49660,138 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -49880,9 +49814,6 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: @@ -50202,13 +50133,118 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:787:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] @@ -50243,8 +50279,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -50256,6 +50290,8 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -50284,6 +50320,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -50304,11 +50341,13 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -50359,218 +50398,9 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5396:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -50697,7 +50527,6 @@ | | | long long unsigned int | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/bitpack64-write.c:5574:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'UINT8' {aka 'long unsigned int'} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ @@ -50790,9 +50619,217 @@ | ~~~~~~~~ | | | UINT8 {aka long unsigned int} +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -50807,7 +50844,6 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -50818,8 +50854,27 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -50838,31 +50893,19 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -50913,14 +50956,22 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -51011,6 +51062,7 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -51018,9 +51070,22 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -51126,43 +51191,14 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -../../src/indexdb.c: In function 'positions_read_multiple': gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c @@ -51206,9 +51242,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -51216,6 +51249,9 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c @@ -51248,6 +51284,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -51268,16 +51305,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -51328,16 +51360,15 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -51435,8 +51466,33 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -51445,6 +51501,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -51468,17 +51525,6 @@ ../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -51506,13 +51552,6 @@ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -51528,16 +51567,9 @@ ../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c: In function 'Compress_compress': ../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:588:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -51567,22 +51599,9 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -51590,6 +51609,23 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c @@ -51633,6 +51669,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -51640,8 +51678,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -51653,18 +51689,31 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); @@ -51676,31 +51725,13 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -51726,6 +51757,7 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -51751,6 +51783,13 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -51850,6 +51889,27 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -51955,36 +52015,12 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c @@ -51993,11 +52029,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c @@ -52038,6 +52074,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c @@ -52049,14 +52093,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c @@ -52100,21 +52136,41 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c @@ -52122,7 +52178,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -52142,32 +52197,13 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); @@ -52194,6 +52230,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -52213,13 +52250,13 @@ ../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c ../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -52245,12 +52282,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -52321,6 +52353,8 @@ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_words': +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -52350,8 +52384,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -52455,6 +52487,12 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -52469,8 +52507,6 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c @@ -52488,9 +52524,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -52498,6 +52531,9 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c @@ -52524,13 +52560,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ @@ -52538,6 +52568,12 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c @@ -52569,9 +52605,6 @@ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -52599,6 +52632,17 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c @@ -52614,14 +52658,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c @@ -52651,16 +52687,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -52708,6 +52734,13 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -52715,9 +52748,8 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:950:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -52743,16 +52775,56 @@ | | | unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +In file included from /usr/include/stdio.h:970, + from ../../src/filestring.h:5, + from ../../src/single-cell.h:9, + from ../../src/single-cell.c:12: +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'input_oneline' at ../../src/single-cell.c:169:14, + inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, + inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, + inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -52761,7 +52833,6 @@ ../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -52774,45 +52845,10 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from ../../src/filestring.h:5, - from ../../src/single-cell.h:9, - from ../../src/single-cell.c:12: -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:404:25, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'fgets', - inlined from 'input_oneline' at ../../src/single-cell.c:169:14, - inlined from 'update_whitelist_counts_text' at ../../src/single-cell.c:412:4, - inlined from 'update_whitelist_counts' at ../../src/single-cell.c:625:10, - inlined from 'Single_cell_compute_priors' at ../../src/single-cell.c:728:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c @@ -52832,114 +52868,89 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' - 3103 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_tree': -../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_intervals': -../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'read_words': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' - 2144 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' - 2150 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read.c: In function 'read_annotations': -../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c: In function 'IIT_debug': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' - 3524 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'read_words_debug': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' - 2288 | FREAD_UINT8(&length8,fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' - 2293 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:241:3, + inlined from 'MD5_compute' at ../../src/md5.c:273:10: +../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 212 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:104:1: note: in a call to function 'transform' + 104 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ +In file included from ../../src/compress-write.c:21: +../../src/compress-write.c: In function 'Compress_cat': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' + 847 | FREAD_UINTS(Buffer,3,fp); + | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -53039,213 +53050,10 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:241:3, - inlined from 'MD5_compute' at ../../src/md5.c:273:10: -../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 212 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:212:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:104:1: note: in a call to function 'transform' - 104 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -In file included from ../../src/compress-write.c:21: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' - 847 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-result.o `test -f 'result.c' || echo '../../src/'`result.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -53254,6 +53062,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -53351,8 +53160,167 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-result.o `test -f 'result.c' || echo '../../src/'`result.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +../../src/access.c: In function 'copy_memory_from_file': +../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -53452,61 +53420,19 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/access.c: In function 'copy_memory_from_file': -../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c ../../src/md5.c:212:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -53515,7 +53441,7 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:321:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -53530,6 +53456,8 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -53538,18 +53466,119 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' + 3103 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_tree': +../../src/iit-read.c:1760:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1761:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1764:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_intervals': +../../src/iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1892:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_words': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' + 2144 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' + 2150 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c -../../src/indexdb.c: In function 'positions_read_multiple_large': -../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1897 | read(positions_high_fd,buffer,1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1901 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'read_annotations': +../../src/iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c: In function 'IIT_debug': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' + 3524 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ +../../src/iit-read.c: In function 'read_words_debug': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' + 2288 | FREAD_UINT8(&length8,fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' + 2293 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c @@ -53563,6 +53592,13 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c +../../src/indexdb.c: In function 'positions_read_multiple_large': +../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1897 | read(positions_high_fd,buffer,1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1901 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c @@ -53603,27 +53639,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 367 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': ../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -53643,6 +53659,26 @@ 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 367 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | read(fd,buf,8); + | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c @@ -53663,12 +53699,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -53682,6 +53712,7 @@ ../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c ../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -53719,10 +53750,25 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c +In file included from ../../src/iit-read.c:12: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' + 2588 | FREAD_INT(&version,fp); + | ^~~~~~~~~ In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -53737,14 +53783,6 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -In file included from ../../src/iit-read.c:12: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' - 2588 | FREAD_INT(&version,fp); - | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -53842,7 +53880,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -53851,6 +53888,7 @@ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -53942,14 +53980,16 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c +../../src/indexdb.c: In function 'positions_read_multiple': +../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1953 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c @@ -53957,10 +53997,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c -../../src/indexdb.c: In function 'positions_read_multiple': -../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1953 | read(positions_fd,buffer,4); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c @@ -53986,14 +54022,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c -In file included from /usr/include/stdio.h:970, - from ../../src/shortread.h:8, - from ../../src/shortread.c:12: -In function 'fgets', - inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c @@ -54002,6 +54030,14 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +In file included from /usr/include/stdio.h:970, + from ../../src/shortread.h:8, + from ../../src/shortread.c:12: +In function 'fgets', + inlined from 'input_oneline.constprop' at ../../src/shortread.c:1145:14: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c @@ -54058,11 +54094,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -54083,30 +54114,13 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 236 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 215 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -54126,6 +54140,17 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:215:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 215 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:299:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 299 | read(fd,buf,4); @@ -54138,8 +54163,19 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': +../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 236 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c @@ -54154,12 +54190,127 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c +In file included from ../../src/transcriptome.c:29: +../../src/transcriptome.c: In function 'Transcriptome_new': +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' + 159 | FREAD_INT(&trnum,fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' + 184 | FREAD_INT(&divint,fp); + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -54210,32 +54361,10 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c -In file included from ../../src/transcriptome.c:29: -../../src/transcriptome.c: In function 'Transcriptome_new': -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:159:5: note: in expansion of macro 'FREAD_INT' - 159 | FREAD_INT(&trnum,fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' - 184 | FREAD_INT(&divint,fp); - | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -54244,6 +54373,7 @@ ../../src/iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -54341,105 +54471,11 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c @@ -54456,11 +54492,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c ../../src/indexdb.c: In function 'positions_read_multiple_large': ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); @@ -54468,6 +54499,11 @@ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c @@ -54484,18 +54520,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -54504,6 +54528,8 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -54512,7 +54538,28 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", @@ -54534,6 +54581,7 @@ | ~~~~~~~~~~~~~ | | | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c ../../src/path.c: In function 'Path_print': ../../src/path.c:3321:29: warning: format '%u' expects argument of type 'unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); @@ -54561,18 +54609,6 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c @@ -54615,10 +54651,6 @@ gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm -gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -54632,6 +54664,7 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm ../../src/stage1hr.c: In function 'Stage1_list_exhaustive': ../../src/stage1hr.c:1333:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1333 | printf("%u %d..%d %d\n", @@ -54666,21 +54699,16 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm +gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx512 gmap_avx512-except.o gmap_avx512-assert.o gmap_avx512-mem.o gmap_avx512-intlist.o gmap_avx512-uintlist.o gmap_avx512-list.o gmap_avx512-littleendian.o gmap_avx512-bigendian.o gmap_avx512-univinterval.o gmap_avx512-interval.o gmap_avx512-stopwatch.o gmap_avx512-semaphore.o gmap_avx512-access.o gmap_avx512-filestring.o gmap_avx512-iit-read-univ.o gmap_avx512-iit-read.o gmap_avx512-md5.o gmap_avx512-bzip2.o gmap_avx512-fopen.o gmap_avx512-sequence.o gmap_avx512-reader.o gmap_avx512-genomicpos.o gmap_avx512-compress.o gmap_avx512-compress-write.o gmap_avx512-gbuffer.o gmap_avx512-genome.o gmap_avx512-popcount.o gmap_avx512-dinucl_bits.o gmap_avx512-genome_canonical.o gmap_avx512-genome-write.o gmap_avx512-bitpack64-read.o gmap_avx512-bitpack64-readtwo.o gmap_avx512-indexdb.o gmap_avx512-oligo.o gmap_avx512-block.o gmap_avx512-chrom.o gmap_avx512-segmentpos.o gmap_avx512-chrnum.o gmap_avx512-uinttable_rh.o gmap_avx512-gregion.o gmap_avx512-match.o gmap_avx512-matchpool.o gmap_avx512-diagnostic.o gmap_avx512-stage1.o gmap_avx512-diag.o gmap_avx512-diagpool.o gmap_avx512-cmet.o gmap_avx512-atoi.o gmap_avx512-orderstat.o gmap_avx512-oligoindex_hr.o gmap_avx512-intron.o gmap_avx512-maxent.o gmap_avx512-maxent_hr.o gmap_avx512-pair.o gmap_avx512-pairpool.o gmap_avx512-cellpool.o gmap_avx512-stage2.o gmap_avx512-doublelist.o gmap_avx512-smooth.o gmap_avx512-splicestringpool.o gmap_avx512-splicetrie_build.o gmap_avx512-splicetrie.o gmap_avx512-boyer-moore.o gmap_avx512-dynprog.o gmap_avx512-dynprog_simd.o gmap_avx512-dynprog_single.o gmap_avx512-dynprog_genome.o gmap_avx512-dynprog_cdna.o gmap_avx512-dynprog_end.o gmap_avx512-translation.o gmap_avx512-pbinom.o gmap_avx512-changepoint.o gmap_avx512-stage3.o gmap_avx512-request.o gmap_avx512-result.o gmap_avx512-output.o gmap_avx512-inbuffer.o gmap_avx512-samheader.o gmap_avx512-printbuffer.o gmap_avx512-outbuffer.o gmap_avx512-chimera.o gmap_avx512-datadir.o gmap_avx512-parserange.o gmap_avx512-getline.o gmap_avx512-gmap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx512 gsnap_avx512-except.o gsnap_avx512-assert.o gsnap_avx512-mem.o gsnap_avx512-intlist.o gsnap_avx512-uintlist.o gsnap_avx512-list.o gsnap_avx512-littleendian.o gsnap_avx512-bigendian.o gsnap_avx512-univinterval.o gsnap_avx512-interval.o gsnap_avx512-stopwatch.o gsnap_avx512-semaphore.o gsnap_avx512-access.o gsnap_avx512-filestring.o gsnap_avx512-iit-read-univ.o gsnap_avx512-iit-read.o gsnap_avx512-bzip2.o gsnap_avx512-reader.o gsnap_avx512-genomicpos.o gsnap_avx512-compress.o gsnap_avx512-genome.o gsnap_avx512-transcriptome.o gsnap_avx512-popcount.o gsnap_avx512-genomebits.o gsnap_avx512-genomebits_consec.o gsnap_avx512-genomebits_count.o gsnap_avx512-genomebits_kmer.o gsnap_avx512-genomebits_indel.o gsnap_avx512-genomebits_decode.o gsnap_avx512-genomebits_mismatches.o gsnap_avx512-genomebits_trim.o gsnap_avx512-dinucl_bits.o gsnap_avx512-genome_sites.o gsnap_avx512-bitpack64-read.o gsnap_avx512-bitpack64-readtwo.o gsnap_avx512-mergeinfo.o gsnap_avx512-merge-diagonals-heap-uint4.o gsnap_avx512-merge-uint4.o gsnap_avx512-merge-diagonals-simd-uint4.o gsnap_avx512-indexdb.o gsnap_avx512-localdb-read.o gsnap_avx512-oligo.o gsnap_avx512-chrnum.o gsnap_avx512-maxent_hr.o gsnap_avx512-mapq.o gsnap_avx512-fopen.o gsnap_avx512-shortread.o gsnap_avx512-junction.o gsnap_avx512-concordance.o gsnap_avx512-simplepair.o gsnap_avx512-orderstat.o gsnap_avx512-intlistpool.o gsnap_avx512-uintlistpool.o gsnap_avx512-listpool.o gsnap_avx512-hitlistpool.o gsnap_avx512-pathpool.o gsnap_avx512-auxinfopool.o gsnap_avx512-pathstorepool.o gsnap_avx512-intron.o gsnap_avx512-gbuffer.o gsnap_avx512-select64-common.o gsnap_avx512-select64-ones.o gsnap_avx512-select64-zeroes.o gsnap_avx512-ef64.o gsnap_avx512-nr-x.o gsnap_avx512-knownsplicing.o gsnap_avx512-knownindels.o gsnap_avx512-splice.o gsnap_avx512-indel.o gsnap_avx512-spliceendsgen.o gsnap_avx512-spliceends.o gsnap_avx512-bitpack64-access.o gsnap_avx512-trdiag.o gsnap_avx512-trdiagpool.o gsnap_avx512-tr-extension-search.o gsnap_avx512-univdiag.o gsnap_avx512-univdiagpool.o gsnap_avx512-sedgesort.o gsnap_avx512-auxinfo.o gsnap_avx512-pathstore.o gsnap_avx512-altsplice.o gsnap_avx512-path.o gsnap_avx512-pathpair.o gsnap_avx512-path-solve.o gsnap_avx512-path-fusion.o gsnap_avx512-path-trim.o gsnap_avx512-path-eval.o gsnap_avx512-pathpair-eval.o gsnap_avx512-path-print-alignment.o gsnap_avx512-path-print-m8.o gsnap_avx512-path-print-sam.o gsnap_avx512-path-learn.o gsnap_avx512-method.o gsnap_avx512-doublelist.o gsnap_avx512-bitvector.o gsnap_avx512-transcriptpool.o gsnap_avx512-exon.o gsnap_avx512-transcript.o gsnap_avx512-trpathpool.o gsnap_avx512-trpath.o gsnap_avx512-trpath-solve.o gsnap_avx512-trpath-convert.o gsnap_avx512-trpath-eval.o gsnap_avx512-transcriptome-search.o gsnap_avx512-vectorpool.o gsnap_avx512-repair.o gsnap_avx512-transcript-remap.o gsnap_avx512-transcript-velocity.o gsnap_avx512-intersect-small.o gsnap_avx512-intersect-uint2.o gsnap_avx512-intersect-approx-uint4.o gsnap_avx512-intersect-approx-indices-uint4.o gsnap_avx512-intersect-wdups-indices.o gsnap_avx512-intersect-lower-small.o gsnap_avx512-intersect-higher-small.o gsnap_avx512-intersect-indices-small.o gsnap_avx512-intersect-indices2-small.o gsnap_avx512-intersect-concordance-uint4.o gsnap_avx512-kmer-search.o gsnap_avx512-extension-search.o gsnap_avx512-repetitive.o gsnap_avx512-uint8table.o gsnap_avx512-uinttable.o gsnap_avx512-stage1hr.o gsnap_avx512-stage1hr-single.o gsnap_avx512-stage1hr-paired.o gsnap_avx512-uinttableuint.o gsnap_avx512-tableuint.o gsnap_avx512-single-cell.o gsnap_avx512-request.o gsnap_avx512-resulthr.o gsnap_avx512-output.o gsnap_avx512-inbuffer.o gsnap_avx512-samheader.o gsnap_avx512-printbuffer.o gsnap_avx512-outbuffer.o gsnap_avx512-uintpairtable.o gsnap_avx512-splice-count.o gsnap_avx512-support.o gsnap_avx512-datadir.o gsnap_avx512-parserange.o gsnap_avx512-getline.o gsnap_avx512-gsnap.o -lz -lbz2 -lm -gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx512 gmapl_avx512-except.o gmapl_avx512-assert.o gmapl_avx512-mem.o gmapl_avx512-intlist.o gmapl_avx512-uintlist.o gmapl_avx512-uint8list.o gmapl_avx512-list.o gmapl_avx512-littleendian.o gmapl_avx512-bigendian.o gmapl_avx512-univinterval.o gmapl_avx512-interval.o gmapl_avx512-stopwatch.o gmapl_avx512-semaphore.o gmapl_avx512-access.o gmapl_avx512-filestring.o gmapl_avx512-iit-read-univ.o gmapl_avx512-iit-read.o gmapl_avx512-md5.o gmapl_avx512-bzip2.o gmapl_avx512-fopen.o gmapl_avx512-sequence.o gmapl_avx512-reader.o gmapl_avx512-genomicpos.o gmapl_avx512-compress.o gmapl_avx512-compress-write.o gmapl_avx512-gbuffer.o gmapl_avx512-genome.o gmapl_avx512-popcount.o gmapl_avx512-dinucl_bits.o gmapl_avx512-genome_canonical.o gmapl_avx512-genome-write.o gmapl_avx512-bitpack64-read.o gmapl_avx512-bitpack64-readtwo.o gmapl_avx512-indexdb.o gmapl_avx512-oligo.o gmapl_avx512-block.o gmapl_avx512-chrom.o gmapl_avx512-segmentpos.o gmapl_avx512-chrnum.o gmapl_avx512-uinttable_rh.o gmapl_avx512-uint8table_rh.o gmapl_avx512-gregion.o gmapl_avx512-match.o gmapl_avx512-matchpool.o gmapl_avx512-diagnostic.o gmapl_avx512-stage1.o gmapl_avx512-diag.o gmapl_avx512-diagpool.o gmapl_avx512-cmet.o gmapl_avx512-atoi.o gmapl_avx512-orderstat.o gmapl_avx512-oligoindex_hr.o gmapl_avx512-intron.o gmapl_avx512-maxent.o gmapl_avx512-maxent_hr.o gmapl_avx512-pair.o gmapl_avx512-pairpool.o gmapl_avx512-cellpool.o gmapl_avx512-stage2.o gmapl_avx512-doublelist.o gmapl_avx512-smooth.o gmapl_avx512-splicestringpool.o gmapl_avx512-splicetrie_build.o gmapl_avx512-splicetrie.o gmapl_avx512-boyer-moore.o gmapl_avx512-dynprog.o gmapl_avx512-dynprog_simd.o gmapl_avx512-dynprog_single.o gmapl_avx512-dynprog_genome.o gmapl_avx512-dynprog_cdna.o gmapl_avx512-dynprog_end.o gmapl_avx512-translation.o gmapl_avx512-pbinom.o gmapl_avx512-changepoint.o gmapl_avx512-stage3.o gmapl_avx512-request.o gmapl_avx512-result.o gmapl_avx512-output.o gmapl_avx512-inbuffer.o gmapl_avx512-samheader.o gmapl_avx512-printbuffer.o gmapl_avx512-outbuffer.o gmapl_avx512-chimera.o gmapl_avx512-datadir.o gmapl_avx512-parserange.o gmapl_avx512-getline.o gmapl_avx512-gmap.o -lz -lbz2 -lm In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -54701,6 +54729,13 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx512 gmap_avx512-except.o gmap_avx512-assert.o gmap_avx512-mem.o gmap_avx512-intlist.o gmap_avx512-uintlist.o gmap_avx512-list.o gmap_avx512-littleendian.o gmap_avx512-bigendian.o gmap_avx512-univinterval.o gmap_avx512-interval.o gmap_avx512-stopwatch.o gmap_avx512-semaphore.o gmap_avx512-access.o gmap_avx512-filestring.o gmap_avx512-iit-read-univ.o gmap_avx512-iit-read.o gmap_avx512-md5.o gmap_avx512-bzip2.o gmap_avx512-fopen.o gmap_avx512-sequence.o gmap_avx512-reader.o gmap_avx512-genomicpos.o gmap_avx512-compress.o gmap_avx512-compress-write.o gmap_avx512-gbuffer.o gmap_avx512-genome.o gmap_avx512-popcount.o gmap_avx512-dinucl_bits.o gmap_avx512-genome_canonical.o gmap_avx512-genome-write.o gmap_avx512-bitpack64-read.o gmap_avx512-bitpack64-readtwo.o gmap_avx512-indexdb.o gmap_avx512-oligo.o gmap_avx512-block.o gmap_avx512-chrom.o gmap_avx512-segmentpos.o gmap_avx512-chrnum.o gmap_avx512-uinttable_rh.o gmap_avx512-gregion.o gmap_avx512-match.o gmap_avx512-matchpool.o gmap_avx512-diagnostic.o gmap_avx512-stage1.o gmap_avx512-diag.o gmap_avx512-diagpool.o gmap_avx512-cmet.o gmap_avx512-atoi.o gmap_avx512-orderstat.o gmap_avx512-oligoindex_hr.o gmap_avx512-intron.o gmap_avx512-maxent.o gmap_avx512-maxent_hr.o gmap_avx512-pair.o gmap_avx512-pairpool.o gmap_avx512-cellpool.o gmap_avx512-stage2.o gmap_avx512-doublelist.o gmap_avx512-smooth.o gmap_avx512-splicestringpool.o gmap_avx512-splicetrie_build.o gmap_avx512-splicetrie.o gmap_avx512-boyer-moore.o gmap_avx512-dynprog.o gmap_avx512-dynprog_simd.o gmap_avx512-dynprog_single.o gmap_avx512-dynprog_genome.o gmap_avx512-dynprog_cdna.o gmap_avx512-dynprog_end.o gmap_avx512-translation.o gmap_avx512-pbinom.o gmap_avx512-changepoint.o gmap_avx512-stage3.o gmap_avx512-request.o gmap_avx512-result.o gmap_avx512-output.o gmap_avx512-inbuffer.o gmap_avx512-samheader.o gmap_avx512-printbuffer.o gmap_avx512-outbuffer.o gmap_avx512-chimera.o gmap_avx512-datadir.o gmap_avx512-parserange.o gmap_avx512-getline.o gmap_avx512-gmap.o -lz -lbz2 -lm +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx512 gsnap_avx512-except.o gsnap_avx512-assert.o gsnap_avx512-mem.o gsnap_avx512-intlist.o gsnap_avx512-uintlist.o gsnap_avx512-list.o gsnap_avx512-littleendian.o gsnap_avx512-bigendian.o gsnap_avx512-univinterval.o gsnap_avx512-interval.o gsnap_avx512-stopwatch.o gsnap_avx512-semaphore.o gsnap_avx512-access.o gsnap_avx512-filestring.o gsnap_avx512-iit-read-univ.o gsnap_avx512-iit-read.o gsnap_avx512-bzip2.o gsnap_avx512-reader.o gsnap_avx512-genomicpos.o gsnap_avx512-compress.o gsnap_avx512-genome.o gsnap_avx512-transcriptome.o gsnap_avx512-popcount.o gsnap_avx512-genomebits.o gsnap_avx512-genomebits_consec.o gsnap_avx512-genomebits_count.o gsnap_avx512-genomebits_kmer.o gsnap_avx512-genomebits_indel.o gsnap_avx512-genomebits_decode.o gsnap_avx512-genomebits_mismatches.o gsnap_avx512-genomebits_trim.o gsnap_avx512-dinucl_bits.o gsnap_avx512-genome_sites.o gsnap_avx512-bitpack64-read.o gsnap_avx512-bitpack64-readtwo.o gsnap_avx512-mergeinfo.o gsnap_avx512-merge-diagonals-heap-uint4.o gsnap_avx512-merge-uint4.o gsnap_avx512-merge-diagonals-simd-uint4.o gsnap_avx512-indexdb.o gsnap_avx512-localdb-read.o gsnap_avx512-oligo.o gsnap_avx512-chrnum.o gsnap_avx512-maxent_hr.o gsnap_avx512-mapq.o gsnap_avx512-fopen.o gsnap_avx512-shortread.o gsnap_avx512-junction.o gsnap_avx512-concordance.o gsnap_avx512-simplepair.o gsnap_avx512-orderstat.o gsnap_avx512-intlistpool.o gsnap_avx512-uintlistpool.o gsnap_avx512-listpool.o gsnap_avx512-hitlistpool.o gsnap_avx512-pathpool.o gsnap_avx512-auxinfopool.o gsnap_avx512-pathstorepool.o gsnap_avx512-intron.o gsnap_avx512-gbuffer.o gsnap_avx512-select64-common.o gsnap_avx512-select64-ones.o gsnap_avx512-select64-zeroes.o gsnap_avx512-ef64.o gsnap_avx512-nr-x.o gsnap_avx512-knownsplicing.o gsnap_avx512-knownindels.o gsnap_avx512-splice.o gsnap_avx512-indel.o gsnap_avx512-spliceendsgen.o gsnap_avx512-spliceends.o gsnap_avx512-bitpack64-access.o gsnap_avx512-trdiag.o gsnap_avx512-trdiagpool.o gsnap_avx512-tr-extension-search.o gsnap_avx512-univdiag.o gsnap_avx512-univdiagpool.o gsnap_avx512-sedgesort.o gsnap_avx512-auxinfo.o gsnap_avx512-pathstore.o gsnap_avx512-altsplice.o gsnap_avx512-path.o gsnap_avx512-pathpair.o gsnap_avx512-path-solve.o gsnap_avx512-path-fusion.o gsnap_avx512-path-trim.o gsnap_avx512-path-eval.o gsnap_avx512-pathpair-eval.o gsnap_avx512-path-print-alignment.o gsnap_avx512-path-print-m8.o gsnap_avx512-path-print-sam.o gsnap_avx512-path-learn.o gsnap_avx512-method.o gsnap_avx512-doublelist.o gsnap_avx512-bitvector.o gsnap_avx512-transcriptpool.o gsnap_avx512-exon.o gsnap_avx512-transcript.o gsnap_avx512-trpathpool.o gsnap_avx512-trpath.o gsnap_avx512-trpath-solve.o gsnap_avx512-trpath-convert.o gsnap_avx512-trpath-eval.o gsnap_avx512-transcriptome-search.o gsnap_avx512-vectorpool.o gsnap_avx512-repair.o gsnap_avx512-transcript-remap.o gsnap_avx512-transcript-velocity.o gsnap_avx512-intersect-small.o gsnap_avx512-intersect-uint2.o gsnap_avx512-intersect-approx-uint4.o gsnap_avx512-intersect-approx-indices-uint4.o gsnap_avx512-intersect-wdups-indices.o gsnap_avx512-intersect-lower-small.o gsnap_avx512-intersect-higher-small.o gsnap_avx512-intersect-indices-small.o gsnap_avx512-intersect-indices2-small.o gsnap_avx512-intersect-concordance-uint4.o gsnap_avx512-kmer-search.o gsnap_avx512-extension-search.o gsnap_avx512-repetitive.o gsnap_avx512-uint8table.o gsnap_avx512-uinttable.o gsnap_avx512-stage1hr.o gsnap_avx512-stage1hr-single.o gsnap_avx512-stage1hr-paired.o gsnap_avx512-uinttableuint.o gsnap_avx512-tableuint.o gsnap_avx512-single-cell.o gsnap_avx512-request.o gsnap_avx512-resulthr.o gsnap_avx512-output.o gsnap_avx512-inbuffer.o gsnap_avx512-samheader.o gsnap_avx512-printbuffer.o gsnap_avx512-outbuffer.o gsnap_avx512-uintpairtable.o gsnap_avx512-splice-count.o gsnap_avx512-support.o gsnap_avx512-datadir.o gsnap_avx512-parserange.o gsnap_avx512-getline.o gsnap_avx512-gsnap.o -lz -lbz2 -lm ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -54733,6 +54768,7 @@ | | | unsigned int | %lu +gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx512 gmapl_avx512-except.o gmapl_avx512-assert.o gmapl_avx512-mem.o gmapl_avx512-intlist.o gmapl_avx512-uintlist.o gmapl_avx512-uint8list.o gmapl_avx512-list.o gmapl_avx512-littleendian.o gmapl_avx512-bigendian.o gmapl_avx512-univinterval.o gmapl_avx512-interval.o gmapl_avx512-stopwatch.o gmapl_avx512-semaphore.o gmapl_avx512-access.o gmapl_avx512-filestring.o gmapl_avx512-iit-read-univ.o gmapl_avx512-iit-read.o gmapl_avx512-md5.o gmapl_avx512-bzip2.o gmapl_avx512-fopen.o gmapl_avx512-sequence.o gmapl_avx512-reader.o gmapl_avx512-genomicpos.o gmapl_avx512-compress.o gmapl_avx512-compress-write.o gmapl_avx512-gbuffer.o gmapl_avx512-genome.o gmapl_avx512-popcount.o gmapl_avx512-dinucl_bits.o gmapl_avx512-genome_canonical.o gmapl_avx512-genome-write.o gmapl_avx512-bitpack64-read.o gmapl_avx512-bitpack64-readtwo.o gmapl_avx512-indexdb.o gmapl_avx512-oligo.o gmapl_avx512-block.o gmapl_avx512-chrom.o gmapl_avx512-segmentpos.o gmapl_avx512-chrnum.o gmapl_avx512-uinttable_rh.o gmapl_avx512-uint8table_rh.o gmapl_avx512-gregion.o gmapl_avx512-match.o gmapl_avx512-matchpool.o gmapl_avx512-diagnostic.o gmapl_avx512-stage1.o gmapl_avx512-diag.o gmapl_avx512-diagpool.o gmapl_avx512-cmet.o gmapl_avx512-atoi.o gmapl_avx512-orderstat.o gmapl_avx512-oligoindex_hr.o gmapl_avx512-intron.o gmapl_avx512-maxent.o gmapl_avx512-maxent_hr.o gmapl_avx512-pair.o gmapl_avx512-pairpool.o gmapl_avx512-cellpool.o gmapl_avx512-stage2.o gmapl_avx512-doublelist.o gmapl_avx512-smooth.o gmapl_avx512-splicestringpool.o gmapl_avx512-splicetrie_build.o gmapl_avx512-splicetrie.o gmapl_avx512-boyer-moore.o gmapl_avx512-dynprog.o gmapl_avx512-dynprog_simd.o gmapl_avx512-dynprog_single.o gmapl_avx512-dynprog_genome.o gmapl_avx512-dynprog_cdna.o gmapl_avx512-dynprog_end.o gmapl_avx512-translation.o gmapl_avx512-pbinom.o gmapl_avx512-changepoint.o gmapl_avx512-stage3.o gmapl_avx512-request.o gmapl_avx512-result.o gmapl_avx512-output.o gmapl_avx512-inbuffer.o gmapl_avx512-samheader.o gmapl_avx512-printbuffer.o gmapl_avx512-outbuffer.o gmapl_avx512-chimera.o gmapl_avx512-datadir.o gmapl_avx512-parserange.o gmapl_avx512-getline.o gmapl_avx512-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx512 gsnapl_avx512-except.o gsnapl_avx512-assert.o gsnapl_avx512-mem.o gsnapl_avx512-intlist.o gsnapl_avx512-uintlist.o gsnapl_avx512-uint8list.o gsnapl_avx512-list.o gsnapl_avx512-littleendian.o gsnapl_avx512-bigendian.o gsnapl_avx512-univinterval.o gsnapl_avx512-interval.o gsnapl_avx512-stopwatch.o gsnapl_avx512-semaphore.o gsnapl_avx512-access.o gsnapl_avx512-filestring.o gsnapl_avx512-iit-read-univ.o gsnapl_avx512-iit-read.o gsnapl_avx512-bzip2.o gsnapl_avx512-reader.o gsnapl_avx512-genomicpos.o gsnapl_avx512-compress.o gsnapl_avx512-genome.o gsnapl_avx512-transcriptome.o gsnapl_avx512-popcount.o gsnapl_avx512-genomebits.o gsnapl_avx512-genomebits_consec.o gsnapl_avx512-genomebits_count.o gsnapl_avx512-genomebits_kmer.o gsnapl_avx512-genomebits_indel.o gsnapl_avx512-genomebits_decode.o gsnapl_avx512-genomebits_mismatches.o gsnapl_avx512-genomebits_trim.o gsnapl_avx512-dinucl_bits.o gsnapl_avx512-genome_sites.o gsnapl_avx512-bitpack64-read.o gsnapl_avx512-bitpack64-readtwo.o gsnapl_avx512-mergeinfo.o gsnapl_avx512-merge-diagonals-heap-uint8.o gsnapl_avx512-merge-uint8.o gsnapl_avx512-merge-diagonals-simd-uint8.o gsnapl_avx512-merge-diagonals-heap-uint4.o gsnapl_avx512-merge-uint4.o gsnapl_avx512-merge-diagonals-simd-uint4.o gsnapl_avx512-indexdb.o gsnapl_avx512-localdb-read.o gsnapl_avx512-oligo.o gsnapl_avx512-chrnum.o gsnapl_avx512-maxent_hr.o gsnapl_avx512-mapq.o gsnapl_avx512-fopen.o gsnapl_avx512-shortread.o gsnapl_avx512-junction.o gsnapl_avx512-concordance.o gsnapl_avx512-simplepair.o gsnapl_avx512-orderstat.o gsnapl_avx512-intlistpool.o gsnapl_avx512-uintlistpool.o gsnapl_avx512-uint8listpool.o gsnapl_avx512-listpool.o gsnapl_avx512-hitlistpool.o gsnapl_avx512-pathpool.o gsnapl_avx512-auxinfopool.o gsnapl_avx512-pathstorepool.o gsnapl_avx512-intron.o gsnapl_avx512-gbuffer.o gsnapl_avx512-select64-common.o gsnapl_avx512-select64-ones.o gsnapl_avx512-select64-zeroes.o gsnapl_avx512-ef64.o gsnapl_avx512-nr-x.o gsnapl_avx512-knownsplicing.o gsnapl_avx512-knownindels.o gsnapl_avx512-splice.o gsnapl_avx512-indel.o gsnapl_avx512-spliceendsgen.o gsnapl_avx512-spliceends.o gsnapl_avx512-bitpack64-access.o gsnapl_avx512-trdiag.o gsnapl_avx512-trdiagpool.o gsnapl_avx512-tr-extension-search.o gsnapl_avx512-univdiag.o gsnapl_avx512-univdiagpool.o gsnapl_avx512-sedgesort.o gsnapl_avx512-auxinfo.o gsnapl_avx512-pathstore.o gsnapl_avx512-altsplice.o gsnapl_avx512-path.o gsnapl_avx512-pathpair.o gsnapl_avx512-path-solve.o gsnapl_avx512-path-fusion.o gsnapl_avx512-path-trim.o gsnapl_avx512-path-eval.o gsnapl_avx512-pathpair-eval.o gsnapl_avx512-path-print-alignment.o gsnapl_avx512-path-print-m8.o gsnapl_avx512-path-print-sam.o gsnapl_avx512-path-learn.o gsnapl_avx512-method.o gsnapl_avx512-doublelist.o gsnapl_avx512-bitvector.o gsnapl_avx512-transcriptpool.o gsnapl_avx512-exon.o gsnapl_avx512-transcript.o gsnapl_avx512-trpathpool.o gsnapl_avx512-trpath.o gsnapl_avx512-trpath-solve.o gsnapl_avx512-trpath-convert.o gsnapl_avx512-trpath-eval.o gsnapl_avx512-transcriptome-search.o gsnapl_avx512-vectorpool.o gsnapl_avx512-repair.o gsnapl_avx512-transcript-remap.o gsnapl_avx512-transcript-velocity.o gsnapl_avx512-intersect-large.o gsnapl_avx512-intersect-small.o gsnapl_avx512-intersect-uint2.o gsnapl_avx512-intersect-approx-uint4.o gsnapl_avx512-intersect-approx-uint8.o gsnapl_avx512-intersect-approx-indices-uint8.o gsnapl_avx512-intersect-wdups-indices.o gsnapl_avx512-intersect-lower-large.o gsnapl_avx512-intersect-higher-large.o gsnapl_avx512-intersect-indices-small.o gsnapl_avx512-intersect-indices2-large.o gsnapl_avx512-intersect-indices-uint8.o gsnapl_avx512-intersect-concordance-uint8.o gsnapl_avx512-kmer-search.o gsnapl_avx512-extension-search.o gsnapl_avx512-repetitive.o gsnapl_avx512-uint8table.o gsnapl_avx512-stage1hr.o gsnapl_avx512-stage1hr-single.o gsnapl_avx512-stage1hr-paired.o gsnapl_avx512-uint8tableuint.o gsnapl_avx512-tableuint.o gsnapl_avx512-single-cell.o gsnapl_avx512-request.o gsnapl_avx512-resulthr.o gsnapl_avx512-output.o gsnapl_avx512-inbuffer.o gsnapl_avx512-samheader.o gsnapl_avx512-printbuffer.o gsnapl_avx512-outbuffer.o gsnapl_avx512-uint8pairtable.o gsnapl_avx512-splice-count.o gsnapl_avx512-support.o gsnapl_avx512-datadir.o gsnapl_avx512-parserange.o gsnapl_avx512-getline.o gsnapl_avx512-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' @@ -54740,41 +54776,41 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build +chmod +x gmap_process +chmod +x gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords -cp psl_splicesites.pl psl_splicesites -cp psl_introns.pl psl_introns -chmod +x gmap_process -chmod +x gmap_build chmod +x gmap_cat -cp psl_genes.pl psl_genes -cp ensembl_genes.pl ensembl_genes chmod +x md_coords chmod +x fa_coords +cp psl_splicesites.pl psl_splicesites chmod +x psl_splicesites +cp psl_introns.pl psl_introns +cp psl_genes.pl psl_genes chmod +x psl_introns +chmod +x psl_genes +cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites +chmod +x ensembl_genes +chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns -chmod +x psl_genes cp gtf_genes.pl gtf_genes -chmod +x ensembl_genes +chmod +x gtf_introns cp gtf_transcript_splicesites.pl gtf_transcript_splicesites +chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns -cp gff3_genes.pl gff3_genes -chmod +x gtf_splicesites -chmod +x gtf_introns -chmod +x gtf_genes -cp dbsnp_iit.pl dbsnp_iit chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites chmod +x gff3_introns -cp gvf_iit.pl gvf_iit +cp gff3_genes.pl gff3_genes +cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_genes +cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit -chmod +x dbsnp_iit chmod +x gvf_iit +chmod +x dbsnp_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/util' Making all in tests @@ -54843,13 +54879,13 @@ /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Tool for genome database creation for GMAP or GSNAP' \ /build/reproducible-path/gmap-2024-11-20+ds/build/util/gmap_build |debian/filter.pl >/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap_build.1 dh_auto_install --builddir build_avx512 - cd build_avx512 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build_avx512 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx512 gmapl.avx512 gsnap.avx512 gsnapl.avx512 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512/src' @@ -54871,18 +54907,18 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx512' dh_auto_install --builddir build_avx2 - cd build_avx2 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build_avx2 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx2 gmapl.avx2 gsnap.avx2 gsnapl.avx2 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2/src' @@ -54904,18 +54940,18 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_avx2' dh_auto_install --builddir build_sse42 - cd build_sse42 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build_sse42 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse42 gmapl.sse42 gsnap.sse42 gsnapl.sse42 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42/src' @@ -54937,26 +54973,26 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse42' dh_auto_install --builddir build_sse41 - cd build_sse41 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build_sse41 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse41 gmapl.sse41 gsnap.sse41 gsnapl.sse41 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41/util' @@ -54970,18 +55006,18 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_sse41' dh_auto_install --builddir build_ssse3 - cd build_ssse3 && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build_ssse3 && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.ssse3 gmapl.ssse3 gsnap.ssse3 gsnapl.ssse3 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3/src' @@ -55003,26 +55039,26 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build_ssse3' dh_auto_install - cd build && make -j42 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build && make -j40 install DESTDIR=/build/reproducible-path/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse2 gmapl.sse2 gsnap.sse2 gsnapl.sse2 '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build/util' @@ -55036,7 +55072,7 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[4]: Entering directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-11-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-11-20+ds/build' @@ -55094,12 +55130,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/301612/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/301612/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2740700 and its subdirectories -I: Current time: Wed Oct 21 09:21:56 -12 2026 -I: pbuilder-time-stamp: 1792617716 +I: removing directory /srv/workspace/pbuilder/301612 and its subdirectories +I: Current time: Fri Sep 19 05:27:01 +14 2025 +I: pbuilder-time-stamp: 1758209221 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/gmap_2024-11-20+ds-2.diff: 94.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/gmap_2024-11-20+ds-2.diff.gz b2/build.log: 94.8% -- replaced with stdout Compressing the 1st log... b1/build.log: 94.8% -- replaced with stdout Thu Sep 18 15:27:05 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_gmap_forky_amd64_1758209225 + touch /var/log/reproducible-builds/diffoscope_stamp_gmap_forky_amd64_1758209225 + RESULT=0 + systemd-run '--description=diffoscope on gmap/2024-11-20+ds-2 in forky/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_2-54672 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI --run-session -c jenkins-reproducible-forky-diffoscope-8090a583-114d-48df-a722-941cce6c5fb2 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/dbd-tmp-8PSsluz ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/gmap_2024-11-20+ds-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/gmap_2024-11-20+ds-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/gmap_2024-11-20+ds-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b1/gmap_2024-11-20+ds-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b2/gmap_2024-11-20+ds-2_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_2-54672.service; invocation ID: 311e99a8b8a34bc6a4c5cb461f9628aa # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/gmap_2024-11-20+ds-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/gmap_2024-11-20+ds-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/gmap_2024-11-20+ds-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b1/gmap_2024-11-20+ds-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wMeJQqBI/b2/gmap_2024-11-20+ds-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 192ms CPU time consumed: 171ms Memory peak: 17.8M (swap: 0B) __ _ _ __ ___ __ _ _ __ / _` | '_ ` _ \ / _` | '_ \ | (_| | | | | | | (_| | |_) | \__, |_| |_| |_|\__,_| .__/ |___/ |_| Thu Sep 18 15:27:06 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 18 15:27:06 UTC 2025 I: gmap from forky built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-18 15:27:06] INFO: Starting at 2025-09-18 15:27:06.444618 [2025-09-18 15:27:06] INFO: Generating the pages of 1 package(s) [2025-09-18 15:27:06] CRITICAL: https://tests.reproducible-builds.org/debian/forky/amd64/gmap didn't produce a buildlog, even though it has been built. [2025-09-18 15:27:06] INFO: Finished at 2025-09-18 15:27:06.695337, took: 0:00:00.250722 Thu Sep 18 15:27:06 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/forky/amd64/gmap.html Thu Sep 18 15:27:06 UTC 2025 I: Removing signed gmap_2024-11-20+ds-2_amd64.buildinfo.asc files: removed './b1/gmap_2024-11-20+ds-2_amd64.buildinfo.asc' removed './b2/gmap_2024-11-20+ds-2_amd64.buildinfo.asc' 1758209226 amd64 forky gmap Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/gmap_2024-11-20+ds-2.rbuild.log: 94.8% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/gmap_2024-11-20+ds-2.rbuild.log.gz [2025-09-18 15:27:07] INFO: Starting at 2025-09-18 15:27:07.198458 [2025-09-18 15:27:07] INFO: Generating the pages of 1 package(s) [2025-09-18 15:27:07] INFO: Finished at 2025-09-18 15:27:07.440746, took: 0:00:00.242291 All cleanup done. Thu Sep 18 15:27:07 UTC 2025 - total duration: 0h 39m 16s. Thu Sep 18 15:27:07 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-UisWDV3F, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 39min 17.633s CPU time consumed: 7.821s Memory peak: 267.3M (swap: 0B)